Methods for Assessing Biological Integrity of Surface Waters in Kentucky Commonwealth of Kentucky Natural Resources and Environmental Protection Cabinet Division of Water Water Quality Branch July 2002 METHODS FOR ASSESSING BIOLOGICAL INTEGRITY OF SURFACE WATERS Kentucky Department for Environmental Protection Division of Water Ecological Support Section Frankfort, Kentucky July 2002 This report has been approved for release: __________________________ Jeffrey W. Pratt, Director __________________________ Date The Natural Resources and Environmental Protection Cabinet does not discriminate on the basis of race, color, national origin, sex, age, religion, or disability, and provides on request, reasonable accommodations including auxiliary aids and services necessary to afford an individual with a disability an equal opportunity to participate in all services, programs and activities. This document was printed on recycled paper with state funds. List of Contributors Ecological Support Section Michael R. Mills Project Leader Gary V. Beck Bacteriologist John F. Brumley Phycologist Samuel M. Call Aquatic Invertebrate Zoologist Michael C. Compton Ichthyologist Eric C. Eisiminger Ichthyologist Gregory J. Pond Aquatic Invertebrate Zoologist Nonpoint Source Section Danny R. Peake Aquatic Invertebrate Zoologist Rodney N. Pierce Fisheries Biologist Stephen E. McMurray Aquatic Invertebrate Zoologist TABLE OF CONTENTS PAGE Chapter 1. Introduction .........................................................................................................1 Chapter 2. Study Plans and Station Selection.......................................................................2 I. Study Plan ..................................................................................................................2 II. Station Selection ........................................................................................................3 Chapter 3. Ecoregions and the Reference Condition............................................................5 I. Introduction to Ecoregions.........................................................................................5 II. Defining Ecoregional Reference Conditions .............................................................9 Chapter 4. Site Characterization ...........................................................................................12 I. Introduction................................................................................................................12 II. Field Data Sheet.........................................................................................................12 Chapter 5. Bacteriological Evaluation ..................................................................................17 I. Introduction................................................................................................................17 II. Bacteriological Sample Collection ............................................................................17 III. Sample Holding Times ..............................................................................................18 IV. General Laboratory Practice ......................................................................................18 V. Interpretation of Bacteriological Analyses ................................................................19 VI. Quality Assurance/Quality Control ...........................................................................19 Chapter 6. Habitat Assessment .............................................................................................21 I. Introduction................................................................................................................21 II. Assessment Procedures..............................................................................................21 III. Parameters for Habitat Assessment ...........................................................................21 IV. Tentative Habitat Criteria ..........................................................................................28 V. Quality Assurance/Quality Control............................................................................30 Chapter 7. Algae ...................................................................................................................31 I. Introduction................................................................................................................31 II. Sampling Procedures .................................................................................................31 III. Sample Preservation and Labeling.............................................................................33 IV. Sample Analysis.........................................................................................................33 V. Data Analysis.............................................................................................................37 VI. Quality Assurance/Quality Control............................................................................42 Phytoplankton ..................................................................................................................43 I. Introduction..........................................................................................................43 II. Sampling Procedures ...........................................................................................43 III. Sampling Preservation .........................................................................................44 IV. Sample Analysis...................................................................................................44 V. Interpretation of Phytoplankton Data...................................................................47 i Chapter 8. Macroinvertebrates..............................................................................................53 I. Introduction................................................................................................................53 II. Sampling Methods .....................................................................................................54 III. Sampling Processing..................................................................................................60 IV. Data Analysis.............................................................................................................61 Chapter 9. Fish Fish Community Structure...............................................................................................72 I. Introduction................................................................................................................72 II. Sampling Methods .....................................................................................................72 III. Laboratory Processing ...............................................................................................74 IV. Quality Assurance/Quality Control............................................................................74 V. Data Analysis.............................................................................................................75 VI. Reporting Fish Data ...................................................................................................79 Chapter 10. Fish & Macroinvertebrate Contaminant Analysis.............................................83 Fish Contaminant Analysis..............................................................................................83 I. Introduction................................................................................................................83 II. Field Sampling Procedures ........................................................................................83 III. Laboratory Procedures...............................................................................................86 IV. Interpretation of Fish Tissue Data..............................................................................86 V. Quality Assurance/Quality Control............................................................................87 Macroinvertebrate Tissue Analysis..................................................................................87 I. Introduction................................................................................................................87 II. Target Species – Sample Preservation-Laboratory Procedures .................................87 III. Quality Assurance/Quality Control............................................................................87 Chapter 11. Nonpoint Source Monitoring ............................................................................92 I. Introduction................................................................................................................92 TABLES PAGE Table 3-1. Summary of physical criteria used in the Reference Reach selection process ..........................................................10 Table 4-1. Substrate Particle Size Chart..........................................................................13 Table 7-1. Microhabitats Usually Found in Wadeable Streams......................................32 Table 7-2. Metric Scoring Formulae for the Diatom Bioassessment Index....................41 Table 8-1. Summary of sampling methods for wadeable, moderate/high gradient streams .......................................................................................57 Table 8-2. Summary of sampling methods for headwater,