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Water: Bioassessment

Chapter 8: Fish Protocols

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This Chapter is divided into two parts: Part A (this file), and Part B

Monitoring of the fish assemblage is an integral component of many water quality management programs, and its importance is reflected in the aquatic life use-support designations of many states. Narrative expressions such as "maintaining coldwater fisheries", "fishable" or "fish propagation" are prevalent in state standards. Assessments of the fish assemblage must measure the overall structure and function of the ichthyofaunal community to adequately evaluate biological integrity and protect surface water resource quality. Fish bioassessment data quality and comparability are assured through the utilization of qualified fisheries professionals and consistent methods.

The Rapid Bioassessment Protocol (RBP) for fish presented in this document, is directly comparable to RBP V in Plafkin et al. (1989). The principal evaluation mechanism utilizes the technical framework of the Index of Biotic Integrity (IBI) -- a fish assemblage assessment approach developed by Karr (1981). The IBI incorporates the zoogeographic, ecosystem, community and population aspects of the fish assemblage into a single ecologically-based index. Calculation and interpretation of the IBI involves a sequence of activities including: fish sample collection; data tabulation; and regional modification and calibration of metrics and expectation values. This concept has provided the overall multimetric index framework for rapid bioassessment in this document. A more detailed description of this approach for fish is presented in Karr et al. (1986) and Ohio EPA (1987). Regional modification and applications are described in Leonard and Orth (1986), Moyle et al. (1986), Hughes and Gammon (1987), Wade and Stalcup 1987, Miller et al. (1988), Steedman (1988), Simon (1991), Lyons (1992a), Simon and Lyons (1995), Lyons et al. (1996), and Simon (1999).

The RBP for fish involves careful, standardized field collection, species identification and enumeration, and analyses using aggregated biological attributes or quantification of the numbers (and in some cases biomass, see Section 8.3.3, Metric 13) of key species. The role of experienced fisheries scientists in the adaptation and application of the RBP and the taxonomic identification of fishes cannot be overemphasized. The fish RBP survey yields an objective discrete measure of the condition of the fish assemblage. Although the fish survey can usually be completed in the field by qualified fish biologists, difficult species identifications will require laboratory confirmation. Data provided by the fish RBP can serve to assess use attainment, develop biological criteria, prioritize sites for further evaluation, provide a reproducible impact assessment, and evaluate status and trends of the fish assemblage.

Fish collection procedures must focus on a multihabitat approach -- sampling habitats in relative proportion to their local representation (as determined during site reconnaissance). Each sample reach should contain riffle, run and pool habitat, when available. Whenever possible, the reach should be sampled sufficiently upstream of any bridge or road crossing to minimize the hydrological effects on overall habitat quality. Wadeability and accessability may ultimately govern the exact placement of the sample reach. A habitat assessment is performed and physical/chemical parameters measured concurrently with fish sampling to document and characterize available habitat specifics within the sample reach (see Chapter 5: Habitat Assessment and Physicochemical Characterization).


All fish sampling gear types are generally considered selective to some degree; however, electrofishing has proven to be the most comprehensive and effective single method for collecting stream fishes. Pulsed DC (direct current) electrofishing is the method of choice to obtain a representative sample of the fish assemblage at each sampling station. However, electrofishing in any form has been banned from certain salmonid spawning streams in the northwest. As with any fish sampling method, the proper scientific collection permit(s) must be obtained before commencement of any electrofishing activities. The accurate identification of each fish collected is essential, and species-level identification is required (including hybrids in some cases, see Section 8.3.3, Metric 11). Field identifications are acceptable; however, voucher specimens must be retained for laboratory verification, particularly if there is any doubt about the correct identity of the specimen (see Section 8.2). Because the collection methods used are not consistently effective for young-of-the-year fish and because their inclusion may seasonally skew bioassessment results, fish less than 20 millimeters total length will not be identified or included in standard samples.


All field team members must be trained in electrofishing safety precautions and unit operation procedures identified by the electrofishing unit manufacturer. Each team member must be insulated from the water and the electrodes; therefore, chest waders and rubber gloves are required. Electrode and dip net handles must be constructed of insulating materials (e.g., woods, fiberglass). Electrofishers/electrodes must be equipped with functional safety switches (as installed by virtually all electrofisher manufacturers). Field team members must not reach into the water unless the electrodes have been removed from the water or the electrofisher has been disengaged.

It is recommended that at least 2 fish collection team members be certified in CPR (cardiopulmonary resuscitation). Many options exist for electrofisher configuration and field team organization; however, procedures will always involve pulsed DC electrofishing and a minimum 2-person team for sampling streams and wadeable rivers. Examples include:

  • Backpack electrofisher with 2 hand-held electrodes mounted on fiberglass poles, one positive (anode) and one negative (cathode). One crew member, identified as the electrofisher unit operator, carries the backpack unit and manipulates both the anode and cathode poles. The anode may be fitted with a net ring (and shallow net) to allow the unit operator to net specimens. The remaining 1 or 2 team members net fish with dip nets and are responsible for specimen transport and care in buckets or livewells.
  • Backpack electrofisher with 1 hand-held anode pole and a trailing or floating cathode. The electrofisher unit operator manipulates the anode with one hand, and has a second hand free for use of a dip net. The remaining 1 or 2 team members also aid in the netting of specimens, and in addition are responsible for specimen transport in buckets or livewells.
  • Tote barge (pramunit) electrofisher with 2 hand-held anode poles and a trailing/floating cathode (recommended for large streams and wadeable rivers). Two team members are each equipped with an anode pole and a dip net. Each is responsible for electrofishing and the netting of specimens. The remaining team member will follow, pushing or pulling the barge through the sample reach. A livewell is maintained within the barge and/or within the sampling reach but outside the area of electric current.

The safety of all personnel and the quality of the data is assured through the adequate education, training, and experience of all members of the fish collection team. At least 1 biologist with training and experience in electrofishing techniques and fish taxonomy must be involved in each sampling event. Laboratory analyses are conducted and/or supervised by a fisheries professional trained in fish taxonomy. Quality assurance and quality control must be a continuous process in fisheries monitoring and assessment, and must include all program aspects (i.e., field sampling, habitat measurement, laboratory processing, and data recording).

Tote barge (pram unit) Electrofishing Backpack Electrofishing
8.1.1 Field Sampling Procedures


  • appropriate scientific collection permit(s)
  • backpack or tote barge-mounted electrofisher
  • dip nets
  • block nets (i.e., seines)
  • elbow-length insulated waterproof gloves
  • chest waders (equipped with wading cleats, when necessary)
  • polarized sunglasses
  • buckets/livewells
  • jars for voucher/reference specimens
  • waterproof jar labels
  • 10% buffered formalin (formaldehyde solution)
  • measuring board (500 mm minimum, with 1 mm increments)a
  • balance (gram scale)b
  • tape measure (100 m minimum)
  • fish Sampling Field Data Sheetc
  • applicable topographic maps
  • copies of field protocols
  • pencils, clipboard
  • first aid kit
  • Global Positioning System (GPS) Unit

a Needed only if program/study requires length frequency information
b Needed only if total biomass and/or the Index of Well-Being are included in the assessment process (see Section 8.3.3, Metric 13).
c It is helpful to copy fieldsheets onto water-resistant paper for use in wet weather conditions.

  1. A representative stream reach (see Alternatives for Stream Reach Designation, next page) is selected and measured such that primary physical habitat characteristics of the stream are included within the reach (e.g., riffle, run and pool habitats, when available). The sample reach should be located away from the influences of major tributaries and bridge/road crossings (e.g., sufficiently upstream to decrease influences on overall habitat quality). The exact location (i.e., latitude and longitude) of the downstream limit of the reach must be recorded on each field data sheet. (If a Global Positioning System unit is used to provide location information, the accuracy or design confidence of the unit should be noted.) A habitat assessment and physical/ chemical characterization of water quality should be performed within the same sampling reach (see Chapter 5: Habitat Assessment and Physicochemical Characterization).
  2. Collection via electrofishing begins at a shallow riffle, or other physical barrier at the downstream limit of the sample reach, and terminates at a similar barrier at the upstream end of the reach. In the absence of physical barriers, block nets should be set at the upstream and downstream ends of the reach prior to the initiation of any sampling activities.
  3. Fish collection procedures commence at the downstream barrier. A minimum 2-person fisheries crew proceeds to electrofish in an upstream direction using a side-to-side or bank-to-bank sweeping technique to maximize area coverage. All wadeable habitats within the reach are sampled via a single pass, which terminates at the upstream barrier. Fish are held in livewells (or buckets) for subsequent identification and enumeration.


    The collection of a representative sample of the fish assemblage is essential, and the appropriate sampling station length for obtaining that sample is best determined by conducting pilot studies (Lyons 1992b, Simonson et al. 1994, Simonson and Lyons 1995). Alternatives for the designation of stream sampling reaches include:

    • Fixed-distance designation--A standard length of stream, e.g., a 150-200-meter reach (Ohio EPA 1987), 100-meter reach (Massachusetts DEP 1995) may be used to obtain a representative sample. Conceptually, this approach should provide a mixture of habitats in the reach and provide, at a minimum, duplicate physical and structural elements such as riffle/pool sequences.
    • Proportional-distance designation-- A standard number of stream channel "widths" may be used to measure the stream study reach, e.g., 40 times the stream width is defined by Environmental Monitoring & Assessment Program (EMAP) for sampling (Klemm and Lazorchak 1995). This approach allows variation in the length of the reach based on the size of the stream. Application of the proportional-distance approach in large streams or wadeable rivers may require the establishment of sampling program time and/or distance maxima (e.g., no more than 3 hours of electrofishing or 500-meter reach per sampling site, [Klemm et al. 1993]).
    • Sampling efficiency is dependent, at least in part, on water clarity and the field team's ability to see and net the stunned fish. Therefore, each team member should wear polarized sunglasses, and sampling is conducted only during periods of optimal water clarity and flow.
    • All fish (greater than 20 millimeters total length) collected within the sample reach must be identified to species (or subspecies).  Specimens that cannot be identified with certainty in the field are preserved in a 10% formalin solution and stored in labeled jars for subsequent laboratory identification (see Section 8.2). A representative voucher collection must be retained for unidentified specimens, very small specimens, new locality records, and/or a particular region. In addition to the unidentified specimen jar, a voucher collection of a subsample of each species identified in the field should be preserved and labeled for subsequent laboratory verification, if necessary. Obviously, species of special concern (e.g., threatened, endangered) should be noted and released immediately on site. Labels should contain (at a minimum) location data (verbal description and coordinates), date, collectors' names, and sample identification code and/or station numbers for the particular sampling site. Young-of-the-year fish less than 20 millimeters (total length) are not identified or included in the sample, and are released on site. Specimens that can be identified in the field are counted, examined for external anomalies (i.e., deformities, eroded fins, lesions, and tumors), and recorded on field data sheets. An example of a "Fish Sampling Field Data Sheet" is provided in Appendix A-4, Form 1. Space is available for optional fish length and weight measurements, should a particular program/study require length frequency or biomass data. However, these data are not required for the standard multimetric assessment. Space is allotted on the field data sheets for the optional inclusion of measurements (nearest millimeter total length) and weights (nearest gram) for a subsample (to a maximum 25 specimens) of each species. Although fish length and weight measurements are optional, recording a range of lengths for species encountered may be a useful routine measure. Following the data recording phase of the procedure, specimens that have been identified and processed in the field are released on site to minimize mortality.


  1. Quality control must be a continuous process in fish bioassessment and should include all program aspects, from field collection and preservation to habitat assessment, sample processing, and data recording. Field validation should be conduced at selected sites and will involve the collection of a duplicate sample taken from an adjacent reach upstream of the initial sampling site. The adjacent reach should be similar to the initial site with respect to habitat and stressors. Sampling QC data should be evaluated following the first year of sampling in order to determine a level of acceptable variability and the appropriate duplication frequency.
  2. Field identifications of fish must be conducted by qualified/trained fish taxonomists, familiar with local and regional ichthyofauna. Questionable records are prevented by: (a) requiring the presence of at least one experienced/trained fish taxonomist on every field effort, and (b) preserving selected specimens (e.g., Klemm and Lazorchak 1995 recommend a subsample of a maximum 25 voucher specimens of each species) and those that cannot by readily identified in the field for laboratory verification and/or examination by a second qualified fish taxonomist (see Section 8.2). Specimens must be properly preserved and labeled (refer to Section 8.1.1, number 5). When needed, chain-of-custody forms must be initiated following sample preservation, and must include the same information as the sample container labels.
  3. All field equipment must be in good operating condition, and a plan for routine inspection, maintenance, and/or calibration must be developed to ensure consistency and quality of field data. Field data must be complete and legible, and should be entered on standardized field data forms and/or digital recorders. While in the field, the field team should possess sufficient copies of standardized field data forms and chains-of-custody for all anticipated sampling sites, as well as copies of all applicable Standard Operating Procedures (SOPs).
  1. The data collection phase includes the completion of the top portion of the "Fish Sampling Field Data Sheet" (Appendix A-4, Form 1), which duplicates selected information from the physical/chemical field sheet. Information regarding the sample collection procedures must also be recorded. This includes method of fish capture, start time, ending time, duration of sampling, maximum and mean stream widths. The percentage of each habitat type in the reach is estimated and documented on the data sheet. Comments should include sampling conditions, e.g., visibility, flow, difficult access to stream, or anything that may prove to be valuable information to consider for future sampling events or by personnel unfamiliar with the site.


  1. A representative voucher collection must be retained for unidentified specimens, small specimens, and new locality records. In addition, a second voucher jar should be retained for a subsample of each species identified in the field (e.g., Klemm and Lazorchak 1995 recommend a subsample of 25 voucher specimens of each species). The vouchers must be properly preserved, labeled, and stored in the laboratory for future reference (see Section 8.2).
  2. Voucher collections should be verified by a second qualified fish taxonomist, i.e., a professional other than the taxonomist responsible for the original field identifications. The word "validated" and the name of the taxonomist that validated the identification should be added to each voucher label. Specimens sent from the laboratory to taxonomic specialists should be recorded in a "Taxonomy Validation Notebook" (see Chapter 7), noting the label information and date sent. Upon return of the specimens, the date received and findings should also be recorded in the notebook (and the voucher label), along with the name of the person who performed the validation.
  3. Information on samples completed (through the identification/validation process) will be tracked in a "Sample Log" notebook, to track the progress of each sample (Appendix A-4, Form 2). Sample log entries will be updated as each step is completed (e.g., receipt, identification, validation, archive).
  4. A library of taxonomic literature is essential for the aid and support of identification/verification activities, and must be maintained (and updated as needed) in the laboratory. A list of selected taxonomic references is provided in Section 8.4.

Fish records of questionable quality are prevented by preserving specimens (that cannot be readily identified in the field) for laboratory examination and/or a voucher collection for laboratory verification. Specimens must be properly preserved (e.g., 10% formalin for tissue fixing and 70% ethanol for long-term storage) and labeled (using museum-grade archival labels/paper, and formalin/alcohol-proof pen or pencil). Labels should contain (at a minimum) site location data (i.e., verbal description and site coordinates), collection date, collector's names, species identification (for fishes identified in the field), species totals, and sample identification code and/or station number. All samples received in the laboratory should be tracked using a sample log-in procedure (Appendix A-4, Form 2). Laboratory fisheries professionals must be capable of identifying fish to the lowest possible taxonomic level (i.e., species or subspecies) and should have access to suitable regional taxonomic references (see Section 8.4) to aid in the identification process. Laboratories that do not typically identify fish, or trained fisheries professionals that have difficulty identifying a particular specimen or group of fish, should contact a taxonomic specialist (i.e., a recognized authority for that particular taxonomic group). Taxonomic nomenclature must be kept consistent and current. Common and scientific names of fishes from the United States and Canada are listed in Robins et al. (1991).


Continue to Ch. 8 (Part B).

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