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Metal Mining Technical Guidance for Environmental Effects Monitoring

Chapter 2

2. Study Design, Site Characterization and General Quality Assurance and Quality Control

2.1 Overview

2.2 Study Design and Site Characterization

2.3 General Quality Assurance / Quality Control and Standard Operating Procedures

2.4 References


2. Study Design, Site Characterization and General Quality Assurance and Quality Control

2.1 Overview

This chapter includes information on study design, site characterization, and general quality assurance / quality control (QA/QC) information for the metal mining environmental effects monitoring (EEM) program. The requirements for the study design and site characterization are listed in the Metal Mining Effluent Regulations (MMER) (Schedule 5, sections (s.) 10–14) and Chapter 1. This includes information such as timelines for EEM studies (first studies, studies aim to confirm absence or presence of effect, magnitude and geographic extent, investigation of cause and final biological monitoring studies prior to a mine closing), content of study-design reports and submission dates. Each chapter of this document contains additional information on recommended methodologies for the study design for fish, fish tissue, benthic invertebrates and alternative method studies. In addition, each chapter provides more detailed information on QA/QC.

2.2 Study Design and Site Characterization

The objective of a study design is to describe how the biological monitoring studies (a fish survey, fish tissue analysis and benthic invertebrate community survey) are to be conducted.

Study designs should describe the following (MMER, Schedule 5, s. 10–14):

  • a summary of previous biological monitoring and effluent and water quality monitoring;
  • information related to site characterization, including the results of plume delineation studies;
  • the objectives of the field monitoring program, including overall approach and rationale for biological monitoring, which may be based on previous monitoring results;
  • statistical design criteria, hypotheses, statistical methods and data needs;
  • a description of how the biological monitoring studies are to be conducted to determine if there are effects, taking confounding influences into consideration;
  • field sampling plans, including what will be measured, where and when it will be measured, location of exposure and reference sites, and rationale for selection of final discharge point;
  • QA/QC measures that will be taken to ensure validity of data; and
  • schedules for field monitoring and submission of the interpretative report.

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2.2.1 Site Characterization

Site characterization information is submitted as part of the EEM study design (MMER Schedule 5, s. 10 (a)). The requirements for site characterization are described in Schedule 5, s. 11 of the MMER. Table 2-1 summarizes site characterization information that should be included in the study design. For the first EEM study design, site characterization is included in detail. For subsequent EEM studies the site characterization can be submitted in summary format, but new information (e.g., production rates) should be updated in detail. In most cases, mines will have most site characterization information available from previous assessments and historical studies. If information critical to the design of the EEM study is not available, additional field data may be required to provide adequate background for the first EEM study design, particularly with respect to hydrology and aquatic resources.

Site characterization information is used to identify suitable sampling areas that have similar habitats in the exposure and reference areas, and to obtain information on other discharges and confounding factors that may affect the interpretation of data obtained from those areas. Information on some of the unique environmental characteristics of mine sites that should be taken into consideration during the site characterization can be found in Section

For mines with insufficient historical information to locate reference and exposure areas, exploratory sampling may be useful. Exploratory sampling can also be used to identify habitat characteristics for effective selection of sampling stations.

An experienced field crew should be able to approximate the effluent field based on field measurements of water quality tracers (e.g., specific conductance) or preliminary dye study results, and can often identify likely depositional areas based on observed receiving water flow and circulation patterns. Thus, it is usually possible to choose some appropriate water and sediment sampling stations in the field and to complete exploratory sampling of the receiving environment concurrent with plume and depositional zone studies and critical resource/habitat inventories in a single campaign.

Much of the site characterization information can be effectively reported in map form. Maps should be of sufficient scale (e.g., 1:5000) to show the features of the study area in adequate detail. The actual scale should be reported on any map used. The geographic extent of the study area to be mapped should be determined on a site-specific basis, and should include the discharge point as well as the exposure and reference areas.

The requirements of the site characterization section of the EEM study design are outlined in the MMER. Additional information relevant to the site characterization that should be reported may include the following (including Table 2-1):

  1. An identification of the major chemical reagents used in the overall production process since January 1, 1996. Mines are encouraged to report current quantities of reagents used. This should list reagents of the following types:
    • activators
    • flocculants
    • pH modifiers
    • depressants
    • frothers
    • collectors
  2. An inventory of all discharge points where effluent is deposited into the exposure area. This inventory should identify all known sources of effluent to the aquatic environment, including those regulated under the MMER, as well as any others (e.g., nonpoint sources) that may have the potential to cause an effect on the aquatic environment.
  3. Information on the local climate, particularly seasonal precipitation patterns.

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Table 2-1: Site characterization information for preparing an EEM study design (text description)
Information TypeRecommended information to be reported (where possible, some of the information can effectively be reported in map form)
General characteristics
  • bedrock and surficial geology
  • topography
  • soil and vegetation
  • site accessibility
  • climatology
  • watershed(s) description
  • water flow (rivers) or dispersion (lakes, estuaries, marine) characteristics
  • general description of how effluent(s) mix(es) with receiving water
  • bathymetry mapping (including slope in marine environments)
  • gradient (rivers)
  • tides (marine) - mean monthly tide height data
  • stratification patterns (thermal and chemical)
  • natural barriers to fish movement
  • effluent plume delineation
Anthropogenic influences
  • docks, wharves, ferry terminals, marinas, boat launches, and public recreational zones
  • bridges, crossings and fordings
  • water intakes, effluent discharges, storm water discharges, sewer overflows
  • waste disposal sites
  • contaminant source inventory, including point- and nonpoint sources
  • dams, culverts, waterfalls and other barriers to fish movement
  • surrounding land use
  • location of aquaculture facilities
Aquatic resource characteristics
  • location of exposure and reference areas used in historical studies
  • fish and shellfish species present (resident and migratory)
  • relative abundance of fish and shellfish species
  • use of the exposure and reference areas by fish and shellfish (spawning grounds, nursery areas, etc.)
  • rare, threatened or endangered fish species (if present)
  • non-commercial fisheries (recreational and subsistence)
  • commercial fisheries
  • zones of macrophyte growth
  • ecologically relevant benthic invertebrate habitat(s) and their relative proportions, including:
    • delineation of depositional and erosional zones
    • substrate classification
Environmental protection systems and practices
  • ater management
  • effluent treatment
  • residence time
  • management of tailings
  • polishing ponds
  • waste rock (including use of waste rock for mine back fill and building material)

Top of Page Plume Delineation

A description of the manner in which the effluent mixes within the exposure area, including an estimate of the concentration of effluent in water at 250 m from each final discharge point (MMER, Schedule 5, s. 11 (a)), is to be described in the site characterization. For subsequent biological monitoring studies the site characterization information may be summarized along with, where applicable, a detailed description of any changes to that information since the submission of the most recent study design (MMER, Schedule 5, s. 19 (1) (a)). This description should include an indication of relative flow of the effluent and receiver, as well as seasonal variations in flow. This will give an indication of dilution rate. The description should also give an indication of the density of the effluent, and where within the water column the effluent is likely to be, prior to complete mixing. This estimate may be based on direct measurements in the field or modelling, but it is recommended that modelling be validated with field measurements.

A fish population study is conducted if the concentration of effluent is greater than 1% in the area located within 250 m of a final discharge point (MMER, Schedule 5, s. 9 (b)). If such a study does not need to be conducted due to the effluent concentration being less than 1%, it is recommended that more rigorous plume delineation methods be used to document the effluent concentrations in the exposure area.

It is recommended that the description of the manner in which effluent mixes within the exposure area include the following:

  • identification of where in the exposure area the effluent is located, prior to mixing with the receiving water;
  • estimation of where in the exposure area the effluent and receiving water begin mixing, and where mixing is complete;
  • estimation of the effluent dilution ratio at points downstream of effluent discharge; and
  • identification of significant sources of dilution, other than the primary receiver (i.e., tributaries or other streams); and
  • how the above vary with the tides and seasons.

For extensive guidance on plume delineation, please consult the Revised Technical Guidance on How to Conduct Effluent Plume Delineation Studies, available from Environment Canada (2003) at This document was prepared for the pulp and paper EEM program but can also be applied to the metal mining EEM program. Additional plume delineation information pertaining to metal mining is discussed below.

Top of Page Measuring of Constituents in the Effluent

Conductivity Surveys

If the conductivity of effluent is consistent during the period of study, a conductivity survey can be used to locate the effluent plume within the exposure area. Survey results can be assessed semi-quantitatively, or conductivity measurements can be converted into relative effluent concentrations lying between 1 (effluent) and zero (background) by applying the following formula:

Cr = (Ca – Cb)/(Ce – Cb)



Ce = effluent conductivity, µS/cm
Cb = background conductivity, µS/cm
Ca = measured conductivity to be converted, µS/cm
Cr = relative concentration

The relative concentration is an expression of the dilution ratio. Temperature readings need to be taken along with the measurements obtained from the conductivity meter, since conductivity rises approximately 2% for every 1°C rise in temperature. Further information on theoretical considerations for effluent plume delineation using conductivity can be found in relevant reference material (e.g., Fischer et al. 1979; Freeze and Cherry 1979).

Although conductivity surveys can provide valid and cost-effective estimates of the location of effluent within the receiving environment, the natural variability of conductivity in surface waters can interfere with locating the edge of the effluent plume. Such natural variability in conductivity may be observed with depth as well as with surface measurements. The presence of multiple tributaries or receiving water bodies can further exacerbate this difficulty.

Tracing by Effluent Metals

The location of the effluent plume within the exposure area may also be estimated by choosing a reference parameter present in the effluent and tracking its fate in time and space by measuring its concentrations in water samples taken at specific locations. The selection of such a tracer needs to be based on its stability and consistency of concentration, as well as on representativeness and ease of measurement. Since the parameter selected has to be a conservative substance, metals such as copper or nickel may serve as a “natural” tracer. Sulphate is often a good tracer of base metal mine effluents, particularly in massive sulphide deposits.

It should be cautioned that the effluent parameter selected for tracing may sometimes be present at the same order of magnitude in receiving waters. This would rule out its application for determining effluent dilution. Other parameters may be specific to the effluent alone, but present in such low concentrations that it makes their detection difficult. Several parameters may be present at significantly greater levels in effluent, which would make them ideal tracers for dilution measurement. However, as a result of complications such as the costs of analysis, instability of the substance, difficulty in measurement, or the lack of an adequate in situ measuring apparatus, these parameters may not always prove to be appropriate “natural” tracers. The potential for effluent metals to be used as tracers for plume delineation should therefore be evaluated on a case-specific basis.

Top of Page Habitat Mapping and Classification

Some elements of habitat mapping and classification, as well as aquatic resource inventory, are included as part of site characterization. More detailed habitat mapping may be helpful in identifying habitat types present in the exposure and reference areas. This section provides guidance on habitat mapping and classification.

The recommended method to create a habitat map is to perform a habitat classification. The recommended framework for classifying aquatic features is the classification system developed by the U.S. Fish and Wildlife Service, Classification of Wetlands and Deepwater Habitats of the United States (Cowardin et al. 1979; Busch and Sly 1992). This system allows for classification of a wide range of continental, aquatic and semi-aquatic habitats. Cowardin et al. (1979) also provide guidance on habitat description for coastal and estuarine situations.

Classification systems for marine shorelines to deep coastal areas include Frith et al. (1993), Booth et al. (1996), Robinson and Levings (1995), Hay et al. (1996) and Robinson et al. (1996). Specifically, estuarine classification has been reviewed by Matthews (1993), Scott and Jones (1995), Finlayson and van der Valk (1995) and Levings and Thom (1994). In the United States, the most widely used system is that of Cowardin et al. (1979) and Cowardin and Golet (1995), with expansions proposed by other authors.

Listed below are examples of environment-specific conditions for various habitats:

Rivers: It is recommended that river habitat descriptions include information on elevation gradient; the location of dams, falls and other barriers to fish migration; mean annual discharge and ranges; and general substrate characteristics of each river (preferably in the form of a gradient profile chart). Upstream and downstream inputs (e.g., storm water, sewer overflow, effluent from other industrial sites) should be mapped and described.

Lakes: Important habitat features of lakes include bathymetry, the locations of major inlets and outlets, and general oxygen-temperature conditions (e.g., thermal stratification, occurrences of oxygen depletion in deep water).

Open coastlines: Suggested additional mapping parameters for open coastlines (marine, Great Lakes) include depth contours, nearshore substrate characteristics, shoreline configuration, and the locations of inflowing rivers and other discharges and activities.

Estuaries: Estuaries are best described in terms of their general salinity gradients, flows, bathymetries and general substrate features. A description of tidal cycles is recommended for all marine and estuary locations. Most of the above features can be described from navigational maps, topographic maps, government publications on tides and river discharge records, and through interviews with local government officials and knowledgeable individuals.

Natural wetlands: A wetland is defined as land that is saturated with water long enough to promote wetland or aquatic processes as indicated by poorly drained soils, hydrophytic vegetation and various kinds of biological activities that are adapted to a wet environment (Metal Mining EEM Review Team 2007). Wetlands include bogs, fens, marshes, swamps and shallow waters (usually two metres deep or less) (Metal Mining EEM Review Team 2007). During the Metal Mining Program Review (2007) the review team recommended that natural wetlands for EEM studies should be avoided. Where a mine final effluent flows into a natural wetland area, EEM studies should be conducted downstream of the wetland when studies upstream are not possible. This recommendation is consistent with the Federal Policy on Wetland Conservation. This policy is found at the website.

It is recommended that bottom substrates be described. Further guidance on aquatic habitat assessment can also be found in the Department of Fisheries and Oceans and the British Columbia Ministry of the Environment and Parks (1987), Orth (1989), Ontario Ministry of Natural Resources (1989), Plafkin et al. (1989), and the Department of Fisheries and Oceans (1990).

Depositional zones in the exposure area should be identified and illustrated on the habitat map. Any information on sediment characterization (chemistry, toxicity) should be reported. Depositional zones occur where water velocity decreases, resulting in particles settling out; the finest particles settle out in the slowest current speeds. Historical contaminant or benthic invertebrate community data may be helpful in identifying sampling stations within a depositional exposure area. To compare resident benthic invertebrate communities, similar (but uncontaminated) sediment depositional zones should be located in the reference area. In situations where historical contamination was from a source other than the mine, two reference areas could be used; one with and one without the historically contaminated sediment.

Top of Page Aquatic Resource Inventory

An aquatic resources inventory includes the identification of fish and shellfish (resident and transient) that are presently being fished commercially and non-commercially (both sport [including stocked fish] and subsistence fishery). The inventory should make particular note of fish species that may be present in sufficient numbers to be considered as a sentinel species, and of utilization (e.g., spawning, nursery) of the exposure area by fish species. In addition, any species recognized by federal, provincial or territorial authorities as rare, threatened or endangered should also be included. The Committee on the Status of Endangered Wildlife in Canada website (; district fisheries biologists in federal, provincial or territorial regulatory or museum agencies; local conservation officials; and members of the local community (fishermen, Aboriginal people and public interest groups) are all sources for this type of information.

The potential success of field programs increases with familiarity of the study area. It is recommended that fieldwork be undertaken to verify historical information if this information is not detailed or recent.

Stocked fish are not appropriate for EEM-type monitoring, as these fish are predominately sport fish and are not appropriate indicator species since their growth and reproduction may be altered depending on how and when they were stocked and raised. As well, stocked fish generally have no apparent reproductive success; therefore, this effect indicator could not be evaluated.

Top of Page Classification Scheme for Reference Area Selection

Because reference areas will vary among different landscapes, approaches have been developed to classify land through which rivers run or in which lakes reside in order to predict aquatic biotic assemblages (Corkum 1989, 1992; Hughes 1995, Maxwell et al. 1995; Omernik 1995). A classification system is a way of simplifying sampling procedures and management strategies by organizing a variable landscape (Conquest et al. 1994). The assumption is that the classification scheme is hierarchical. The advantage of a hierarchical classification scheme is that it “offers a way to discriminate among features of the landscape at several scales of resolution” (Conquest et al. 1994). The classification scheme is based (with modifications) on one developed by the U.S. Department of Agriculture’s Forest Service (Maxwell et al. 1995). The hierarchical classification scheme is presented as a guide in the a prioriselection of sampling areas.

Habitat-Specific Allocation of Reference and Exposure Areas

The following specific points should be considered during the selection of reference and exposure areas and/or stations:

For Rivers:

  • The size of the drainage basin selected is based on stream order. For example, if a mine site is located on a second-order stream, the drainage basin area is delineated at the point the stream becomes third-order (i.e., at the junction of two second-order streams).
  • If there are no upstream inputs or confounding factors, reference area(s) can be within the drainage basin and upstream of the mine.
  • If confounding factors, such as nonpoint- or point-source inputs, occur upstream of the effluent, the reference area(s) can be selected in nearby drainage basins with comparable habitat features (Figure 4-4).
  • If physical disturbance of the river valley is associated with the mine, effluent effects may be confounded by the disturbance. Accordingly, reference areas should be selected to match the physical disturbance, if possible.
  • The following features should be similar between reference and exposure areas: ecoregion, drainage basin area, stream order, bankfull width, channel gradient, channel pattern, habitat types, water depth, water velocity, substratum composition, riparian vegetation, shoreline structure and land use, etc.

For Lakes:

  • In lakes with a single-mine effluent and without nonpoint sources of pollution, the sphere of influence originating from the effluent should be determined. This is particularly important for lakes in which effluent flow is not unidirectional.
  • If effluent plume delineation and former studies indicate that mine effects are likely to be local and restricted, select reference areas within the lake in which the mine discharge occurs. These reference areas should occur in separate but comparable bays or basins of the lake.
  • If effluent plume delineation indicates that the identified effluent is dispersed throughout the lake, select reference area(s) in the nearest comparable lake within the same or adjacent drainage basin.
  • If nonpoint- or other point-source inputs occur elsewhere on a lake, select reference area(s) in the nearest comparable lakes within the same or adjacent drainage basin.
  • If the mine effluent is associated with physical disturbance in the area, effluent effects may be confounded by the disturbance. Accordingly, physically matched reference areas should be selected, if possible.
  • The following features should be similar between reference and exposure areas: ecoregion, geological origin, drainage basin area, morphometry, slope from shoreline, habitat types, substratum composition, riparian vegetation, shoreline structure and land use, etc.

For Marine Environments:

  • The reference area should be within the same water body and hydrographic current or tidal regime as the exposure area. In other words, the closer the reference area is to the exposure area, the better. Benthic invertebrate communities in marine ecosystems are considerably higher in species richness, have more complex trophic relationships, faunal size ranges and reproductive strategies, than benthic invertebrate communities in freshwater ecosystems. Because of this complexity, and the multitude of interactions between species in marine benthic invertebrates, small shifts in physical or chemical conditions can dramatically alter the overall benthic faunal community. Add to this the effect of increasing variation in chance larval settlement with increasing geographic distance (geographic “drift” in community structure) and physical barriers in complex coastlines, and it is very rare to find similar invertebrate communities from one bay or fjord to the next, and very difficult to predict specific benthic community structure based on sediment factors (for recent review on marine invertebrate sediment interactions, see Snelgrove and Butman 1994)). In order to have some confidence that the “natural” benthic community is similar enough from one coastal area to the next, there should be sufficient water exchange between them. This is more likely in open coastal areas than in isolated bays and fjords.
  • Reference areas that are not in the same water body or hydrographic regime may only be suitable for comparisons of summary characters such as shifts in abundance or species richness. If the habitat conditions are similar enough to the exposure area, it may also be possible to compare larger-scale biotic factors such as the presence of characteristic, long-lived depth/substrate specific taxa described by Thorson (1957) as “parallel communities”.
  • Reference and exposure areas should have very similar habitat type, shoreline structure (steep, mountainous, delta, marsh, etc.), bottom topography (sills, sandbars, exposure to open oceanic influences, etc.), substrate type (particle size, sorting, natural chemistry), depth properties, current regimes, physical water properties, nutrient regimes, confounding inputs and drainage characteristics.
  • Some special considerations are important for determining the suitability of reference areas for marine and estuarine mines. Physical factors in the estuarine/marine environment that tend to be more complex than in freshwater are salinity (including seasonal freshwater influence), tides (and tidal currents) and sediment sulphides. Other important physical factors include ice-scour or buildup, freezing, water column stagnation due to large summer freshwater runoff, re-suspension due to surface freezing in winter, dams or log-booms, extraordinary siltation or clogging from logging, and periodic flooding.
  • In addition to the above important characteristics, the following specific points should be similar between reference and exposure areas:
    • intertidal areas: shoreline slope, wave exposure, light and tidal exposures, shoreline vegetation, and encrusting fauna (although the latter may be part of the benthic taxa being monitored for a response to mine effluent).
    • sub-tidal areas: seasonal water column stability and bottom oxygen depletion (stagnation).


The first step in reference site selection is to use terrestrial attributes (ecoregions) with similar features. Ecoregions are defined as “part of an ecoprovince characterized by distinctive ecological responses to climate as expressed by vegetation, soils, water, and fauna” (Wiken 1986; Wickware and Rubec 1989). Ecoregion maps for Canada are available here.

Drainage Basin and Geographic Scale

Catchments or drainage basins have clear hydrographic boundaries. A drainage basin is defined as the area that has a common outlet for its surface runoff. Although inter-basin transfer occurs among biota, the geoclimatic history of large basins (1:2 000 000) are known to create barriers to dispersal through hydrographic divides and climate (Maxwell et al. 1995). It is essential to establish the geographic scale appropriate to the study design. In large-scale, synoptic surveys in which relationships are sought between landscape features and aquatic biota, the mapping scale for drainage basins is 1:250 000 (Corkum 1989, 1992, 1996; Reynoldson and Rosenberg 1996). These basins are subdivided into progressively smaller sub-basins.

Land/water interactions with respect to sediment and nutrient transport off the land and from upstream sources is integral in developing predictive models that link environmental variables and associated biota. Drainage basins may occur within ecoregions or may cross different ecoregions. Aquatic fauna are more similar to one another in drainages that occupy the same ecoregion than in drainages that occupy different ecoregions (Corkum 1992; Hughes et al. 1994).

Land Use and Vegetative Buffer Strips

Although ecoregions are defined in terms of climate and natural vegetation, natural vegetation is disturbed with human development. Land-use type is a simple measure of disturbance within the drainage basin. If there is a change in land use (e.g., land clearing for agricultural uses or logging, or fire), the biological assemblages in receiving waters will respond to those changes (Corkum 1992, 1996). Accordingly, site selection should be in drainages with comparable land use.

The degree (width and type) of a vegetated buffer strip adjacent to rivers and lakes should be recorded at all sampling areas. In reference areas where human disturbance cannot be avoided, the effect of a vegetated buffer strip moderates temperature fluctuations through shading (Budd et al. 1987), removes or reduces sediment from runoff (Young et al. 1980), and regulates nutrients and metals entering the water body (Peterjohn and Correll 1984).

Top of Page Framework for Rivers

The river sampling design provides a framework for characterizing habitats at multiple scales (Meador et al. 1993). The framework for rivers is based on how they are organized in hierarchical space and how they change through time (Frissell et al. 1986). The riverine system has several hierarchical or nested levels: drainage or catchment basin, valley segment, stream reach and channel unit (Conquest et al. 1994).

Valley Segment and Stream Order

Valley segments are distinctive sections of drainage basins that possess geomorphic properties and hydrological transport characteristics that distinguish them from other segments (Cupp 1989). Montgomery and Buffington (1993) identified three valley segment types: colluvial (channelized and unchannelized), alluvial and bedrock. Valley segments can be filled with colluvium (sediment and organic matter from landslides) or alluvium (sediment transported by flow). The third valley segment has little soil and is dominated by bedrock.

Valley segments are distinguished by six criteria (Conquest et al. 1994):

  1. Stream order (position in drainage network)
  2. Valley slide-slope gradient
  3. Ratio of valley bottom width to active channel width
  4. Channel gradient
  5. Stream-corridor geomorphic surface deposits
  6. Channel pattern.

Channel segments are assigned stream orders (Strahler 1957) for a particular map scale or aerial photograph (e.g., 1:250 000) (Newbury and Gaboury 1993).

Stream Reach

Stream reaches consist of homogeneous associations of topographic features and channel geomorphic units (Bisson and Montgomery 1996). Stream reaches can be used to predict local stream response to perturbations (Montgomery and Buffington 1993). Stream reaches are useful in assessing habitat quality, aquatic productivity, fish distributions and stream health (Maxwell et al. 1995). Stream reach classification is determined using map scales of 1:12 000 to 1:24 000. Criteria used to classify stream reaches include:

  • channel pattern
  • channel entrenchment
  • channel width
  • hydraulic radius
  • basin area
  • channel material
  • stream gradient
  • bed form
  • riparian vegetation

Simpler approaches have been adopted to identify stream reaches. For example, a straight channel has an undulating bed with alternating riffles and pools spaced at repeating intervals of 5-7 channel widths (Leopold et al. 1964; Leopold 1994). Newbury (1984) defined a stream reach to be equivalent to six times the channel width.

Channel Unit

Channel units are subdivisions of stream reaches that describe uniform microhabitats (depth and flow) and are used to identify factors that limit both invertebrate and fish populations within a stream reach. Hawkins et al. (1993) proposed a three-tiered system of channel units in which the first level distinguishes riffles from pools. The second level identifies turbulent and non-turbulent riffles and distinguishes between pools formed by scour or dams. Dammed pools retain more sediment and organic debris and have more cover than scour pools. The third subdivision identifies microhabitats based on hydraulic processes and structure. Channel units are typically 10 m or less and typically cannot be mapped at a scale appropriate for land management.

Criteria for subdivision of riffles include:

  • gradient or water surface profile
  • percentage of super-critical flow
  • bed roughness
  • mean velocity
  • step development

Criteria for subdivision of pools include:

  • location (main channel or off-channel)
  • longitudinal and cross-sectional depth profiles
  • substrate characteristics
  • pool-forming constraints

Top of Page Framework for Lakes

The geological origin, hydrology and morphometry (obtained from maps and aerial photographs) of lakes are important in identifying sediment-water interactions and productivity of lakes (Wetzel 1975). Although thermal stratification can be predicted from morphological features, field verification is necessary. The mapping scale for lakes is typically 1:24 000 or 1:63 000 (Maxwell et al. 1995).

Origins, Location and Hydrological Linkages

Reference and exposure lakes should have the same origin, location and hydrological linkages. Lake geology ultimately affects the physical, chemical and biological characteristics of water bodies. For example, Hutchinson (1957) identifies 11 types of geomorphic processes (tectonic, volcanic, landslides, glacial activity, solution, fluviatile, wind, shorelines, organic accumulation, anthropogenic and natural dams, meteorite impact). Surface geology and location (altitude, latitude and longitude) affect lake chemistry and thermal regimes (Winter 1977). These variables, which can be obtained from maps, are used to predict the biological composition and productivity of lakes (Dolman 1990; Winter and Woo 1990). Hydrological linkage refers to the “connection of a lake to surface or ground water” and can forecast information about lake biota (Maxwell et al. 1995). Maxwell et al. (1995) describe three types of hydrological linkages: riverine linkage (outlets and/or inlets or unconnected), groundwater linkage (gaining, losing, neutral or no recharge), and water storage regime (perennial or intermittent).


Lake morphometry has been used historically to predict fish yields (Ryder 1965; Kerr and Ryder 1988) and to determine species diversity (Eadie and Keast 1984; Marshall and Ryan 1987). With the exception of depth (and volume), other features can be obtained from maps. Hypsographic (cumulative depth-area or cumulative depth-volume) graphs are useful for comparing basin shapes of lakes and predicting surface area or volume for water-level control of reservoirs. Common morphological features of lakes include surface area, volume, mean and maximum depth, shoreline development, and hydraulic residence time.

Trophic State

Many lake classification systems are based on a measure of productivity (oligotrophy, mesotrophy, eutrophy). A fourth lake type (dystrophy) is used to describe lakes that receive large amounts of organic matter from external sources; these lakes are heavily stained and are known as brown-water lakes. Productivity of dystrophic lakes is low and so some limnologists group dystrophic lakes as a subclass of oligotrophic lakes. The following variables have been used to describe the trophic status of lakes:

  • dissolved oxygen
  • thermal mixing (lake stratification)
  • total phosphorus
  • soluble reactive phosphorus
  • total nitrogen
  • nitrite + nitrate
  • ammonium
  • chlorophyll a
  • transparency
  • organic matter


Lakes are subdivided into an open-water pelagic zone, a shoreline or littoral zone inhabited by autotrophic vegetation, and a deeper benthic region free of vegetation (the profundal zone). The reference and exposure areas should always be located in the same zone.

Top of Page Use of Sublethal Toxicity for Site Characterization

Since historical sublethal toxicity data for some or all of the required tests (see Chapter 6) have been generated for effluents discharged from a number of mine sites across Canada, the operator may want to use this information during site characterization in the following ways:

  1. To aid in determining sampling areas for fish or the benthic invertebrate community. If the operator has no historical field data on fish, fish food sources or fish habitat from their effluent exposure zone, historical effluent sublethal toxicity data (if available in sufficient quality) could be used to estimate the potential zone of influence to help in establishing sample collection locations for the fish and benthic invertebrate community surveys in the first biological monitoring (i.e., estimation of extent of response in the high effluent exposure area). Details on how to estimate the geographic extent of a sublethal toxicity response are provided in Chapter 6.
  2. As an aid in comparing effluent discharge sources. If there are numerous effluent discharge locations at a mine site, one of the recommended sublethal toxicity tests could be used to quantify the degree of sublethal toxicity contributed from the different effluent discharge sources (see chapter 6).

Top of Page Characteristics of Mining Environments

Many mines and mining activities share some similarity in environmental features. They are briefly outlined below:

Headwater location of mine sites: Many mine sites are located near the headwaters of rivers or streams. In some instances the effluent can constitute a significant portion of the flow downstream of the discharge point. This will have an impact on how to characterize the mine’s exposure area. Headwater streams, because of their size, gradient or intermittent flow, are often not suitable fish habitat. Therefore, the mine effluent is frequently discharged to receiving waters with small or no fish populations, although the diluted effluent will, in most cases, eventually reach fish habitat. Nonetheless, some fish species often use accessible headwater areas at some stage of their life cycle, such as for spawning, and this information should be considered when designing an EEM study. Mines may have to move progressively downstream until they reach an area with suitable number and species of fish; however mines should assess fish populations in the immediate receiving environment first.

Effluent quality and volume: Effluent quality and quantity are influenced by several factors including the nature of the ore and host rock, processing methods, effluent treatment methods, climate, and site hydrology. Discharge rates will vary both in volume and duration based on site-specific factors. In Canada, some mining operations discharge seasonally. Reduced natural degradation of substances such as cyanide and ammonia under cold conditions sometimes makes it difficult to achieve discharge limits; therefore, wastewater is discharged during spring and summer. Wastewater may also be discharged during early spring to release large quantities of snow meltwater that has accumulated during the winter months.

The presence of fish in the initial receiving environment can also be a factor in the discharge of effluent volume. For example, the need to protect overwintering fish in pools when natural stream flow is minimal may cause a mine to reduce its effluent discharge to the exposure area. Other mines minimize discharges in late summer when stream flow is low and fish may be spawning. Conversely, spring discharge rates may be high, allowing water inventories to be relieved while stream flows are high. However, not all mines have sufficient reservoir capacity to optimize effluent releases.

Mine ore bodies are variable, resulting in variations in effluent discharges. Each ore is different, not only between mines but also within each mine itself. One ore body may contain more or less of certain minerals. In addition, while mines may have a short life span, the mill at the mine site may process ore from several mines. Virtually every mine has its own distinct suite of parameters of concern in effluents that influence site-specific factors related to bioavailability and hardness. However, similarities in operations among mines in a region may allow for efficiencies to be realized by a regional EEM study design.

Mines incorporate a variety of effluent treatment options (e.g., lime addition, settling ponds, water treatment plants) in their processes, and the type and effectiveness of each treatment option will influence the effluent discharged to the environment. The retention time in tailings ponds can affect the composition of the effluent. For example, cyanide breakdown and settlement of particulate matter are time-dependent. A sufficiently long residence time can potentially modify the concentrations in the effluent.

Local geology: Mine location is determined by the regional geology and the exact locations of ore deposits. Local mineralization around ore deposits influences the natural background levels of metals in streams. The net result is often a naturally higher background concentration of metals in streams located near mine sites, which should be considered during reference area selection such that comparability to the exposure area is optimized.

Bioavailability of metals: The bioavailability of metals is an important aspect to consider when assessing the effects of mine effluent in the EEM program, as ongoing research continues to identify modifying factors that can change their bioavailability. For example, the effects of soluble metals on the biota can be mitigated during effluent treatment (e.g., adding lime to precipitate metals). In addition, the effect of mine effluent and associated sediments on the aquatic environment can vary during the mine’s life cycle as the bioavailability of certain parameters changes.

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2.2.2 Exposure and Reference Areas

An area is qualitatively defined for sampling purposes and relates to the appropriate geographical scale encompassing one or more fundamental sampling locations (“stations”). A station is a fixed sampling location that can be recognized, re-sampled and defined quantitatively (e.g., latitude/longitude). Within EEM, the overall study area is subdivided into reference and exposure areas (for control-impact designs) or within an exposure area where there are gradually decreasing effluent concentrations (for gradient designs). The MMER definition of exposure area is “all fish habitat and waters frequented by fish that are exposed to effluent,” and the definition of reference area is “water frequented by fish that is not exposed to effluent and that has fish habitat that, as far as practical, is most similar to that of the exposure area.” (MMER, Schedule 5, s. 1). Selection of Final Discharge Point for Monitoring

In cases where the mine has more than one final discharge point, it is recommended that sampling be done in an exposure area where the effluent has the greatest potential to have an adverse effect on the receiving environment. The mass loadings of the deleterious substances, the manner in which the effluent mixes in the exposure area, and the sensitivity of the receiving environment should all be considered when selecting which final discharge point should be used for biological monitoring.

Top of Page Selection of Exposure and Reference Areas

The selection of the sampling areas is one of the most critical components of the study design and should be considered carefully to maximize the quality of the information gained from the study. The design of biological surveys is site-specific, and various examples of potential study designs are presented in Chapter 4. However, this guidance is not intended to limit the mine’s flexibility to propose other potential study designs that may be suitable to the site. Exposure Area

Exposure area sampling should be done in an area proximate to the effluent discharge where effects may be found. Sampling areas should ideally support both appropriate habitat for the benthic invertebrate community and populations of the selected fish species. The study design should also consider the use of the exposure area by fish species (e.g., spawning, nursery). Identification of the exposure area and its habitat features should precede the selection of reference areas, because reference areas will, as far as practicable, match the physical and chemical habitat features of the exposure area (other than the features expected to change due to the effluent).

The exposure area may extend through a number of receiving environments (e.g., different stream orders, lakes or marshes, estuarine to marine, or intertidal to sub-tidal) and contain a variety of habitat types. In most cases, the boundary of the exposure area is defined by the zone of effluent mixing. Within an exposure area, there may be a high effluent and a low effluent exposure area often referred to as near-field and far-field areas, respectively. Additional sampling areas within the exposure area may be used during phases to assess magnitude and geographic extent of effects, or during periodic monitoring to provide an enhanced study or address site-specific needs. High effluent exposure (near-field) areas are outside the initial discharge zone (as described below) and have higher exposure to effluent than far-field areas. The initial discharge zone is the area where the effluent exceeds the velocity of the receiving water and the effluent is buoyant. The initial discharge zone is often characterized by visual turbulence and typically does not extend more than 5-50 m from the outfall. At least one of the high effluent exposure (near-field) stations should be as near as possible to the effluent discharge point but located outside the initial discharge zone. For magnitude and geographic extent studies, the exposure area extends along the effluent gradient so that additional lower effluent exposure areas (far-field areas) are included. The exposure area extends geographically until a return to reference area conditions (regulatory definitions of exposure and reference areas are provided above). Lower effluent exposure areas are recommended to be positioned close to the boundary of the zone of effluent mixing. Multiple sampling stations in each defined area should be used to determine spatial variation. In a gradient design, there is no reference area per se, but the response variables are evaluated along the effluent gradient.

In practical use, there will probably always be one or more low effluent exposure (far-field) areas for media other than fish (e.g., water, sediment and benthos). Recommended positioning of low effluent (far-field) exposure areas should be such that each area differs in regard to degree of effluent exposure. If possible, all exposure areas should be located so as to minimize or avoid exposure to non-mine discharges.

Top of Page Reference Area

Reference areas do not need to represent pristine (pre-European settlement) conditions, but, rather, can comprise areas in which anthropogenic impacts, unrelated to the mine effluent, are similar to exposure areas (Simon 1991; Omernik 1995).Where feasible, the reference area should be located in the same water body as the effluent discharge, upstream of or beyond any influence from the discharge. The reference area should be suitable physically and biologically, and outside the influence of the mine or other confounding factors. When a mine is located at a headwater, and/or where no suitable reference area on the same water body is available (e.g., dams and reservoirs may be upstream), the reference area should be located in an adjacent water body with similar characteristics or a non-impacted tributary to the receiving water body. Another possibility is sampling a number of exposure areas at increasing distances from the discharge point, representing an exposure gradient (gradient design). More than one reference area may be used, where appropriate. During magnitude and geographic extent studies, it may be necessary to sample more than one reference area if multiple exposure areas with different habitat types are sampled. As well, a more regional approach could be considered, particularly for benthic invertebrate community surveys, such as looking at several non-impacted streams (or lakes) in the area (i.e., reference condition approach).

Where historical monitoring data exist, the mine should consider using the same sampling areas from previous studies, provided they are appropriate for use in the EEM program. This will help ensure that monitoring data collected as part of the EEM program may be compared with historical data.

Baseline data (pre-effluent discharge) and multiple reference areas may assist in data interpretation. It is possible to use historical data as a baseline comparison to determine effects, but it should be treated as data additional to the mine’s own. The mine’s design should therefore include both a reference area and an exposure area (or follow a gradient design). This ensures that reference conditions have not changed and that changes observed are not incorrectly attributed to the mine, because there can be changes in parameters related to changes in environmental conditions (e.g., due to flooding or variability in annual temperatures). A reference area should be used to allow characterization of those changes that are mine-related compared to those that are not. Practitioners can also take advantage of the environmental assessment phase for new projects to provide information complimentary to the EEM program (Kilgour et al. 2007).

Where possible, sampling areas for different components (fish, benthic invertebrate community, water) should be co-located. The characteristics of the selected fish species, (e.g., mobility, habitat usage) and the different sampling gear may not always make this practical. The reference areas for benthic invertebrate sampling in some cases can be directly upstream of the exposure area, which may not be the case with fish (due to mobility). In addition, mines are encouraged to conduct benthic invertebrate community and fish monitoring studies concurrently, if justifiable biologically (e.g., if the ideal time for sampling fish reproductive parameters coincides with a suitable time for benthic community sampling; see Chapter 3 for additional information on timing for fish reproduction). Where there is more than one mine in close proximity and effluents are discharged to the same drainage basin, joint EEM studies are encouraged. Where studies are proposed jointly, sampling areas may be shared.

Data obtained from reference areas when compared to exposure areas can detect impairment of aquatic life (Yoder 1991), diagnose stressors (Hughes et al. 1994), provide data on temporal and spatial trends (Yoder 1989) and provide data for water resource summaries for government agencies (OEPA 1990). The identification of “least impacted” areas will differ across the country. Reference areas in extremely disturbed areas may be impossible to locate. Here, studies should be designed so that reference areas with minimal degradation are located in comparable drainage basins within the same ecoregion (Hughes et al. 1994).

Usually, coastal mines do not have strictly “upstream” areas for reference sampling, because of variable directionality of current due to tidal effects. Estuarine mines may have upstream areas that are too different physically and biologically to be suitable for reference sampling. The reference area is therefore usually at least periodically downstream from the effluent discharge. Accordingly, it is important to understand the current flow patterns in the area to determine whether a potential reference area is “outside” mine effluent exposure.

Selection of a reference area in the initial phase should not necessarily dictate its use in future phases.

In selecting sampling areas, the mine should take the following factors into consideration:

  • the location of sampling areas in previous surveys;
  • the location of confounding influences;
  • the size of area needed to accommodate the number of samples to be collected;
  • habitat type;
  • site access; and
  • other issues that could affect the mobility of fish.

In general, both sampling areas should be as follows:

  • As similar as possible except for exposure to effluent. Although the two areas are unlikely to be identical, it is assumed that the differences in natural characteristics (e.g., depth, substrate, flow and water quality) will, other than mine-related factors, be small relative to the potential effect associated with the presence of effluent. If this is not the case, it should become apparent, and study design changes should be made in subsequent phases.
  • Situated as closely as possible to each other (but sufficiently distant to be confident that fish from the reference area are not exposed to effluent).
  • Accessible, and offer safe sampling during the most appropriate season (i.e., when measurements on fish growth, reproduction, condition and survival can be taken).
  • Described in as much detail as possible, including the latitude and longitude as well as a written description of the area (physical, chemical and biological habitat, including measurements of temperature, depth and flow).

At a minimum, for a control/impact study, sampling should be conducted at no less than 1 reference area and 1 exposure area during the first EEM study, and subsequent EEM studies (studies aim to confirm presence or absence of effect and magnitude and geographic extent). The use of multiple reference areas offers the greatest statistical power to detect a meaningful difference between a reference area and an exposure area (Foran and Ferenc 1999). It can also give an indication of variability among reference areas (Munkittrick et al. 2000). Differences found in the exposure area that are outside the range of values seen at a number of reference areas are more likely to be ecologically relevant (Munkittrick et al. 2000). Sampling multiple reference areas is preferred over increasing sample size (e.g., number of fish) at a single area (Environment Canada 1997).

When possible there are advantages to selecting similar sampling areas for benthic and fish sampling so that the data can be used to help interpret responses. However, optimal benthic sampling areas may be inappropriate for the fish survey because of the characteristics of the fish species selected, the mobility of the fish, different habitat selection, and the type of sampling gear required. The sampling areas may be the same in many circumstances, but this should not be a sufficient criterion in itself for selecting the fish sampling area.

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2.2.3 Reporting of Field Station Positions

The interpretative report shall contain the latitude and longitude of sampling areas in degrees, minutes and seconds; a description of the sampling areas sufficient to identify them is required (MMER Schedule 5, s. 17(b)). The latitude and longitude coordinates can be obtained using a variety of methods. Global positioning systems are a common tool for locating the position of field stations and are recommended for this purpose. In some instances, the coordinates with stream-wise distances (e.g., river kilometres) may be useful. The recommended positioning accuracy should be determined on a site-specific basis. In some cases, where there are multiple outfalls, industrial sites may decide to collaborate on their studies.

Additional stations may be included to better represent spatial patterns in a large zone of effluent mixing, such as at a location with transects (right, mid, left), and reference/high effluent exposure area (near-field) /low effluent exposure areas (far-field) sampling areas.

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2.2.4 Modifying or Confounding Factors

Modifying or confounding factors can alter the interpretation of the results of biological monitoring. If the sampling areas are fairly similar, effects of modifying factors can be considered negligible. However, when there are significant differences among sampling areas, the survey design becomes confounded. In this case, it may be difficult to differentiate the effects of mine effluent from the effects of the modifying factor(s) on the response variable. For example, if the habitat type (e.g., pool) downstream of the mine was different from the habitat found upstream (e.g., riffle), the effects of habitat type on variables would confound any effects related to mine effluent; both mine effluent and habitat type may be good predictors of any differences in variables observed upstream and downstream of the effluent discharge.

Incorporating multiple reference locations into the study design can aid in designing against spatial confounding factors, and practitioners are encouraged to do so. Design considerations for the detection of anthropogenic disturbances have been presented in the literature (see Green 1993 and references therein; Underwood 1994; Underwood 1997), and practitioners are encouraged to incorporate these considerations into their study designs.

Some examples of potential confounding factors include:

  • tributaries and other point- and nonpoint-source discharges (e.g., other industrial discharges, agricultural runoff, aquaculture facilities, sewage treatment plants);
  • natural environmental/habitat variables; and
  • historical damage.

Attention to potential confounding factors identified during site characterization should be considered during the study design. In this way confounding factors can be minimized, or accounted for in the study design so that their influence can be assessed during data interpretation.

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2.2.5 Tributaries and Other Point- and Nonpoint-Source Discharges

Tributaries provide dilution water to a main channel, lake, estuary or open ocean. This dilution water may or may not have similar chemical properties to the water body under study. Tributaries also require time and distance to mix with the water body under study. Therefore, if there is a tributary between the reference and exposure area, the additional flow from the tributary can potentially confound the interpretation of data.

Other point- and nonpoint-source discharges may make it difficult to distinguish between effects due to the mine effluent and other discharges, particularly if they are found within close proximity to the mine effluent discharge. When other discharges are present immediately above the mine, multiple reference areas should be used. One reference area should be set between the other discharge and the effluent discharge. In this way it may be possible to account for the influence of the other discharge. As well, the reference area should have similar background levels of metals. If no differences between the two reference areas are found, they can be pooled to compare against the exposure area.

If there are other point-source effluent discharges not related to mines in the study area, the study design should attempt to minimize the potential effects of the confounding factors. When it is not possible to resolve the confounding factors by modifying the study design, alternative sampling designs and methods should be evaluated.

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2.2.6 Natural Variation in Environmental or Habitat Conditions

Natural biological communities can differ both temporally and spatially. Particularly if study areas are extensive, it is possible that natural biological communities and characteristics will be different from one location to another. It may be difficult to distinguish the influences of mine effluent, if any, relative to natural variation.

Examples of common, naturally occurring and sometimes confounding factors include:

  • habitat type (riffle, run, pool);
  • substrate type (organic content, particle size);
  • water depth;
  • water flow rate/discharge;
  • tidal action / currents / wave exposure;
  • salinity;
  • dissolved oxygen/temperature;
  • emergent/submergent vegetation cover;
  • water chemistry (conductivity, hardness, pH, etc.); and
  • biological properties.

Once present in the study design, confounding effects cannot be eliminated. Only by giving careful attention to potential modifying factors identified during the pre-design phase or the previous phases of the survey can the influence of modifying factors be removed or controlled in subsequent phases. Where it is not possible to eliminate confounding factors, increasing the number of sampling areas or including additional chemical and/or biological parameters may allow the investigator to assess their influence on data interpretation.

When it is not possible to resolve the confounding factors by modifying the study design, alternative sampling designs and methods (Chapter 9) should be considered.

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2.2.7 Historical Damage

When the area in which a mine releases its effluent has been subject to damage from previous activities, it may be difficult to determine differences due to current effluent-release practices. The use of an alternative method may have to be used in these situations.

2.3 General Quality Assurance / Quality Control and Standard Operating Procedures

2.3.1 Quality Assurance and Quality Control

Detailed QA/QC is described in each chapter. QA/QC is a documented system incorporating adequate review, audit and internal quality control. The objective of a QA/QC program is to ensure that all field sampling and laboratory analyses produce technically sound and scientifically defensible results.

QA is a planned system of operations and procedures, the purpose of which is to provide assurance to the client that defined standards of quality are being met. Analytical QA defines the way in which tasks are to be performed in order to ensure that data meet predefined data quality goals. These tasks include not only the analysis itself but all aspects of sample handling and data management.

QA encompasses a wide range of internal and external management and technical practices designed to ensure data of known quality commensurate with the intended use of the data. External QA activities include participation in relevant inter-laboratory comparisons and audits by outside agencies. Outside audits may be based on performance in analysis of standard reference materials, or on general review of practices as indicated by documentation of sampling, analytical and QA/QC procedures, test results, and supporting data. QC is an internal aspect of QA. It includes the techniques used to measure and assess data quality and the remedial actions to be taken when data quality objectives (DQOs) are not realized. Within the context of a particular study, assurance of adequate data quality is only possible when DQOs have been defined. Users of the data should play a lead role in defining DQOs for a study and in ascertaining whether laboratory quality-control limits are consistent with these objectives.

Data quality measures should be defined in the same terms as DQOs, so that the two can be compared in project evaluation. DQOs are normally derived from intended data uses (e.g., hypotheses to be tested, summary statistics involved, and total uncertainty that can be tolerated). Total uncertainty includes imprecision (sampling, analytical, environmental) plus any analytical bias that may occur (Taylor 1987). Objectives can be established for each component and for total uncertainty, and should be incorporated into the QA project plans. The various components of imprecision can be estimated using field replicate data and laboratory replicate data.

QA functions, the personnel responsible for each QA function, and corrective actions when performance limits are exceeded should be identified in the quality management plan.

QC activities define the boundaries of acceptable performance for the measurement system, and include the routine checks (data quality measures) that indicate whether the system is performing to specification. Data reporting generally stops and corrective actions are initiated when the system goes out of control. Range and average-control charting methods have been described elsewhere (OMOE 1984; ASTM 1985, 1986; Dux 1986).

An outline of recommended QA/QC requirements for specific components of the fish survey (Chapter 3), benthic invertebrate survey (Chapter 4), effluent and water quality analysis (Chapter 5), and sediment quality analysis (Chapter 7) are presented in each respective chapter. This information focuses on QC in the field, laboratory, data analysis, and reporting.

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2.3.2 Standard Operating Procedures

Standard operating procedures (SOPs) are fundamental to any QA/QC program. All field and lab procedures should be conducted according to SOPs to ensure quality control. SOPs should describe the following in detail:

  • the field program’s requirement for sampling methods and procedures, sample handling, labelling, equipment, preserving, record keeping, and shipping; and
  • the analytical methods and procedures, sample handling, labelling, equipment, test system implementation, record keeping and so forth of all laboratory analyses.

Each SOP should be a written, detailed method accessible to each analyst. SOPs should be based on procedures developed by a standard-setting organization such as Environment Canada, the U.S. Environmental Protection Agency, the American Society for Testing and Materials, or the American Public Health Association. Where methods are not well validated, it is recommended that the SOP be thoroughly referenced to the relevant literature and contain all the elements outlined in CALA (1991). In-house validation of data should be appended to the SOP and should contain the QA/QC procedures, including the types and frequencies of QC samples to be analyzed, expected levels of precision, accuracy and recovery, and the method detection limits.

While chemical analysis procedures tend to be reasonably well documented, sampling procedures in general, and sampling design in particular, are often overlooked. Sampling error is usually a large component and often the dominant component of uncertainty in environmental measurements. SOPs that include field operations will help to reduce this uncertainty or at least ensure that it is quantified. All field staff should be familiar with the SOPs for any field survey work.

Emphasis should be placed on measures to prevent inadvertent contamination of samples and to ensure sample integrity. In addition, SOPs should specify the proper preparation of all sampling gear and supplies, and the proper calibration of all instrumentation (such as meters).

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2.4 References

[ASTM] American Society for Testing and Materials. 1985. Standard practice for establishing conditions for laboratory sensory evaluation of foods and beverages. Philadelphia (PA): American Society for Testing and Materials. ASTM E480-84.

[ASTM] American Society for Testing and Materials. 1986. Physical requirement guidelines for sensory evaluation laboratories. Philadelphia (PA): American Society for Testing and Materials. ASTM STP 913.

Bisson PA, Montgomery DR. 1996. Valley segments, stream reaches, and channel units. In Hauer FR, Lamberti GA, editors. Methods in stream ecology. San Diego (CA): Academic Press. p. 23-52.

Booth J, Hay D, Truscott J. 1996. Standard methods for sampling resources and habitats in coastal subtidal regions of British Columbia: Part I - Review of mapping with preliminary recommendations. Canadian Technical Report of Fisheries and Aquatic Science 2118.

Budd WW, Cohen PL, Saunders PR, Steiner FR. 1987. Stream corridor management in the Pacific Northwest: 1. Determination of stream-corridor widths. Environ Manag 11:587-597.

Busch W-DN, Sly PG, editors. 1992. The development of an aquatic habitat classification system for lakes. Boca Raton (FL): CRC Press.

[CALA] Canadian Association for Laboratory Accreditation: formerly CAEAL (Canadian Association of Environmental Analytical Laboratories). 1991. Code of practice and QA manual for laboratory analysis of sewage treatment effluent in support of the MISA Program; Draft report prepared for CAEAL and the Ontario Ministry of the Environment by Zenon Environmental Laboratories.

Conquest LL, Ralph SC, Naiman RJ. 1994. Implementation of large-scale stream monitoring efforts: sampling design and data analysis issues. In Loeb SL, Spacie A, editors. Biological monitoring of aquatic systems. Boca Raton (FL): Lewis Publ. p. 69-90.

Corkum LD. 1989. Patterns of benthic invertebrate assemblages in rivers of northwestern North America. Freshwat Biol 21:191-205.

Corkum LD. 1992. Spatial distributional patterns of macroinvertebrates along rivers within and among biomes. Hydrobiologia 239:101-114.

Corkum LD. 1996. Responses of chlorophyll a, organic matter and macroinvertebrates to nutrient additions in rivers flowing through agricultural and forested land. Arch Hydrobiol 136:391-411.

Cowardin LM, Carter V, Golet FC, LaRoe ET. 1979. Classification of wetlands and deepwater habitats of the United States. U.S. Fish and Wildlife Service. FWS/OBS-79/31.

Cowardin LM, Golet CF. 1995. US Fish and Wildlife Service 1979 wetland classification: a review. Vegetatio 118:139-152.

Cupp CE. 1989. Valley segment type classification for forested lands of Washington. Timber, Fish & Wildlife AM-89-001.

Department of Fisheries and Oceans. 1990. Coastal/estuarine habitat description and assessment manual. Part II. Habitat description procedures. Coquitlam (BC): Prepared by G.L. Williams and Associates Ltd.

Department of Fisheries and Oceans and British Columbia Ministry of the Environment and Parks. 1987. Fish Habitat Inventory and Information Program: Stream Survey Field Guide.

Dolman WB. 1990. Classification of Texas reservoirs in relation to limnology and fish community associations. Trans Am Fish Soc 119:511-520.

Dux JP. 1986. Handbook of quality assurance for analytical chemistry laboratory. New York (NY): Van Nostrand Reinhold Co.

Eadie JM, Keast A. 1984. Resource heterogeneity and fish species diversity in lakes. Can J Zool 62:1689-1695.

Environment Canada. 2003. Revised technical guidance on how to conduct effluent plume delineation studies. Available from:

Environment Canada. 1997. Fish Survey Expert Working Group report. EEM/1997/6.

Finlayson CM, van der Valk AG. 1995. Wetland classification and inventory. A summary. Vegetatio 118(1-2)185-192.

Fischer HB, List EJ, Koh RCY, Imberger J, Brooks NH. 1979. Mixing in inland and coastal waters. San Diego (CA): Academic Press Inc.

Foran J, Ferenc S. 1999. Multiple stressors in ecological risk and impact assessment. Pensacola (FL): SETAC Press.

Freeze RA, Cherry JA. 1979. Groundwater. Englewood Cliffs (NJ): Prentice-Hall.

Frissell CA, Liss WL, Warren CE, Hurley MD. 1986. A hierarchical framework for stream habitat classification: Viewing streams in a watershed context. Environ Manag 10:199-214.

Frith HR, Seraring G, Wainwright P, Harper H, Emmett B. 1993. Review of habitat classification systems and an assessment of their suitability to coastal B.C. Unpub. report to Environment Canada from L.G.L. Ltd., Sidney (BC).

Green RH. 1993. Application of repeated measures designs in environmental impact and monitoring studies. Australian J Ecol 18:81-98.

Hay DE, Waters RD, Boxwell, editors. 1996. Proceedings Marine Ecosystem Monitoring Network Workshop, Nanaimo, B.C. March 28-30. 1995. Canadian Technical Report of Fisheries and Aquatic Science 2108.

Hawkins CP, Kershner JL, Bisson PA, Bryant MD, Decker LM, Gregory SV, McCullough DA, Overton CK, Reeves GH, et al. 1993. A hierarchical approach to classifying stream habitat features. Fisheries 18:3-12.

Hughes RM. 1995. Defining acceptable biological status by comparing with reference conditions.. InDavis WS, Simon TP, editors. Biological assessment and criteria: tools for water resource planning and decision making. Boca Raton (FL): Lewis Publishers. p. 31-47.

Hughes RM, Heiskary SA, Matthews WJ, Yoder CO. 1994. Use of ecoregions in biological monitoring. In Loeb SL, Spacie A, editors. Biological monitoring of aquatic systems. Boca Raton (FL): Lewis Publ. p. 125-149.

Hutchinson GE. 1957. A treatise on limnology. Vol I. Geology, physics, and chemistry. New York (NY): John Wiley & Sons Inc.

Kerr SR, Ryder RA. 1988. The applicability of fish yield indices in freshwater and marine ecosystems. Limnol Oceanogr 33:973-981.

Kilgour BW, Dubé MG, Hedley K, Portt CB, Munkittrick KR. 2007. Aquatic environmental effects monitoring guidance for environmental assessment practitioners. Environ Monit Assess 130:423-436.

Leopold LB. 1994. A view of the river. Cambridge (MA): Harvard University Press.

Leopold LB, Wolman GM, Miller JP. 1964. Fluvial processes in geomorphology. San Francisco (CA): W.H. Freeman & Co.

Levings CD, Thom RM. 1994. Habitat changes in the Georgia Basin: Implications for resource management and restoration. In Wilson RCH, Beamish RJ, Aitkens F, Bell J, editors. Review of the marine environment and biota of Strait of Georgia, Puget Sound and Juan de Fuca Strait: Proceedings of the BC/Washington Symposium on the Marine Environment, Jan 13,14 1994. Canadian Technical Report of Fisheries and Aquatic Science 1948. p. 330-351.

Marshall TR, Ryan PA. 1987. Abundance and community attributes of fishes relative to environmental gradients. Can J Fish Aquat Sci 44:196-215.

Matthews GWT. 1993. The Ramsar Convention: its history and development. Glan (CH): Ramsar Convention Bureau.

Maxwell JR, Edwards CJ, Jensen ME, Paustian SJ, Parrott H, Hill DM. 1995. A hierarchical framework of aquatic ecological units in North America (Nearctic Zone). St. Paul (MN): U.S. Department of Agriculture, Forest Service, North Central Forest Experimental Station. Gen. Tech. Rep. NC-176.

Meador MR, Hupp CR, Cuffney TF, Gurtz ME. 1993. Methods for characterizing stream habitat as part of the national water-quality assessment program. Raleigh (NC): U.S. Geological Survey. Open-File Report 93-408.

Metal Mining EEM Review Team. 2007. Report of the Metal Mining EEM Review Team. Available from:

Montgomery DR, Buffington JM. 1993. Channel classification, prediction of channel response, and assessment of channel condition. Olympia (WA): Department of Natural Resources. Washington State Timber/Fish/Wildlife Agreement. Report TFW-SH10-93-002.

Munkittrick KR, McMaster M, Van Der Kraak G, Portt C, Gibbons W, Farwell A, Gray M. 2000. Development of methods for effects-based cumulative effects assessment using fish populations: Moose River Project. Pensacola (FL): SETAC Press.

Newbury RW. 1984. Hydrological determinants of aquatic insect habitats. InResh VH, Rosenberg DM, editors. The ecology of aquatic insects. New York (NY): Praeger. p. 323-357.

Newbury RW, Gaboury MN. 1993. Stream analysis and fish habitat design. A field manual. Newbury Hydraulics Ltd., The Manitoba Habitat Heritage Corporation, Manitoba Fisheries Branch.

[OEPA] Ohio Environmental Protection Agency. 1990. Ohio water resource inventory. Columbus (OH): Ohio Environmental Protection Agency.

Omernik JM. 1995. Ecoregions: a spatial framework for environmental management. In Davis WS, Simon TP, editors. Biological assessment and criteria. Tools for water resource planning and decision making. Boca Raton (FL): Lewis Publishers. p. 49-62.

Ontario Ministry of Natural Resources. 1989. Manual of Instructions. Aquatic Habitat Inventory Surveys. Toronto (ON): Ontario Ministry of Natural Resources.

[OMOE] Ontario Ministry of the Environment. 1984. Principles of control charting. King DE, Ronan RC, editors. Laboratory Services Branch, Data Quality Report Series. Rexdale (ON): Ontario Ministry of the Environment.

Orth DJ. 1989. Aquatic habitat measurements. In Neilson LA, Johnson DL, editors. Fisheries Techniques. Bethesda (MD): Am. Fish. Soc. p. 61-84.

Peterjohn WT, Correll DL. 1984. Nutrient dynamics in an agricultural watershed: observation on the role of a riparian forest. Ecology 65:1466-1475.

Plafkin JL, Barbour MT, Porter KD, Gross SK, Hughs RM. 1989. Rapid bioassessment protocols for use in streams and rivers: benthic macroinvertebrates and fish. EPA/444/4-89-001.

Reynoldson TD, Rosenberg DM. 1996. Sampling strategies and practical considerations in building reference data bases for the prediction of invertebrate community structure. In Bailey RC, Norris RH, Reynoldson TB, editors. Study design and data analysis in benthic macroinvertebrate assessments of freshwater ecosystems using a reference site approach. Technical Information Workshop North American Benthological Society, 44th Annual Meeting, Kalispell, Montana. p. 1-31.

Robinson CLK, Levings CD. 1995. An overview of habitat classification systems, ecological models and geographic information systems applied to shallow foreshore marine habitats. Canadian Management Report of Fisheries and Aquat Science 2322.

Robinson CLK, Hay DE, Booth J, Truscott J. 1996. Standard methods for sampling resources and habitats in coastal subtidal regions of British Columbia: Part 2 - Review of sampling with preliminary recommendations. Canadian Technical Report of Fisheries and Aquatic Science 2119.

Ryder RA. 1965. A method for estimating the potential fish production of north temperate lakes. Trans Am Fish Soc94:214-218.

Scott DA, Jones TA. 1995. Classification and inventory of wetlands. Vegetatio 118:1-16.

Simon TP. 1991. Development of biotic integrity expectations for the ecoregions of Indiana. I. Central Corn Belt Plain. U.S. Chicago (IL): Environmental Protection Agency, Region V, Environmental Sciences Division, Monitoring and Quality Assurance Branch. Ambient Monitoring Section. EPA 905/9-91/025.

Snelgrove RVR, Butman CA. 1994. Animal sediment relationships revisited: cause versus effect. Oceanogr Mar Biol Ann Rev 32:111-178.

Strahler AN. 1957. Quantitative analysis of watershed geomorphology. Am Geophys Union Trans 38:913-920.

Taylor JK. 1987. Quality assurance of chemical measurements. Chelsea (MI): Lewis Publishers Inc.

Thorson G. 1957. Bottom communities(sublitorral or shallow shelf). In Hedgpeth JW, editor. Treatise on marine ecology and paleoecology. Vol 1. Memoirs of the Geological Society of America 67. p. 461-534.

Underwood AJ. 1994. On beyond BACI: sampling designs that might reliably detect environmental disturbances. Ecol Applications 4(1):3-15.

Underwood AJ. 1997. Experiments in ecology: their logical design and interpretation using analysis of variance. Cambridge University Press. United Kingdom.

Wetzel RG. 1975. Limnology. Philadelphia (PA): W.B. Saunders Co.

Wickware GM, Rubec CDA. 1989. Ecoregions of Ontario. Ecological Land Classification Series 26. Environment Canada.

Wiken E. 1986. Terrestrial ecotones of Canada. Ecological Land Classification Series 19. Ottawa (ON): Environment Canada.

Winter WT. 1977. Classification of hydrological settings of lakes in the north-central United States. Water Resources Research 134:753-767.

Winter WT, Woo MK. 1990. Hydrology of lakes and wetlands.. In Wolman MG, Riggs HC, editors. Surface water hydrology. Boulder (CO): The Geological Society of America. p. 159-187.

Yoder CO. 1989. The development and use of biological criteria for Ohio surface waters.. In Water quality standards for the 21st century. Washington (DC): U.S. Environmental Protection Agency, Office of Water. p. 139-146.

Yoder CO. 1991. Answering some concerns about biological criteria based on experiences in Ohio. In Water quality standards for the 21st century. Washington (DC): U.S. Environmental Protection Agency, Office of Water. p. 95-104.

Young RA, Huntrods T, Anderson W. 1980. Effectiveness of vegetated buffer strips in controlling pollution from feedlot runoff. J Environ Qual 9:483-497.


Table 2-1 provides additional information relevant to the site characterization that should be reported when preparing an EEM study design. The primary information types include general characteristics, hydrology, anthropogenic influences, aquatic resource characteristics, and environmental protection systems and practices. Each information type is accompanied by a list of recommended information to be reported.

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