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Thomas R. Payne & Associates is now part of the employee owned Normandeau Associates team.  We are the same professional staff with the expanded resources of a nationally recognized company providing high quality, practical environmental solutions.  Visit our Normandeau website also.

Fisheries Biology, Consulting, and Software Publishing
890 L Street, Arcata, California USA 95521
P.O. Box 4678, Arcata, California USA 95518
(707) 822-8478

Thomas R. Payne & Associates, Firm Profile


Thomas R. Payne & Associates is a fisheries consulting firm with extensive experience in the analysis of instream flow needs and the impacts of water resource project development on fishery resources.  Over the past eighteen years, TRPA has worked on nearly 200 separate projects, conducting instream flow studies, modeling instream water temperatures, evaluating fish habitat and populations, developing fish habitat use criteria curves, designing and constructing fish habitat enhancement structures, conducting watershed cumulative impact analyses, negotiating fishery resource protection provisions, preparing licensing documents, and completing environmental impact reviews and assessments.  Projects on which TRPA has participated range in scope from backyard fish rearing ponds to billion dollar destination resort complexes, located on intermittent high mountain creeks to major navigable rivers with average annual flow of 32,000 cubic feet per second.


TRPA, located in Arcata on the Redwood Coast of Northern California, has performed fisheries research throughout the Pacific Northwest and Rocky Mountain States, New England and the East Coast, and Hawaii and Guam, with an emphasis on northern and central California. Humboldt State University and its nationally-known School of Natural Resources and Sciences provides TRPA with assistance from eminent professors, experienced and dedicated graduate student labor, and the resources of an extensive fisheries library.


The types of services performed by TRPA include:


Instream Flow Analysis - TRPA has been involved in all phases of applying and reviewing Instream Flow Incremental Methodology studies, from project impact scoping, assessment method selection, and flow study performance, to computer analysis using PHABSIM, results negotiation and interpretation, and final project mitigation design.  TRPA staff has extensive experience designing and conducting habitat suitability criteria studies for a wide variety of aquatic species. 


TRPA also offers training, workshops, and University classes in the application of PHABSIM with microcomputer software developed by TRPA. TRPA’s software, called RHABSIM (Riverine HABitat SIMuation), is a fully integrated program for river hydraulics and aquatic habitat modeling using the Instream Flow Incremental Methodology. Running in Microsoft Windows and DOS, it is an extensive conversion of the PHABSIM hydraulic and habitat simulation system developed by the U. S. Fish and Wildlife Service.


Water velocities, stream channel profile measurements, and water surface elevations are elements of IFIM data collection.


Habitat Criteria Development - Habitat Suitability Criteria (HSC) are an integral component of instream flow modeling using PHABSIM, 2D models, or other habitat-based modeling approaches.  Despite the direct and significant effects of HSC on estimating the flow-habitat relationship, relatively little guidance is available to assist flow modelers in the development and/or evaluation of HSC.  Consequently, the old adage of “garbage-in, garbage-out” is a real possibility.  Thomas R. Payne & Associates has been involved with the development of site-specific HSC curves for 25 species in over 60 rivers within the U.S., Canada, and the tropical Pacific.  Projects have occurred in small headwater streams, large mainstem rivers, and remote tropical streams, involving a diverse assemblage of warmwater, coldwater, anadromous, and resident fish species in summer and winter conditions.  This breadth of experience from collecting new HSC data, testing transferability of existing HSC, and conducting fish counts has made TRPA highly adaptable and we are leaders in studies involving snorkeling and scuba methodologies.



Habitat suitability criteria data are collected in many habitats, not just those suitable to the field biologists.


Water Temperature Modeling  - TRPA has experience applying the Stream Network Temperature Model in mainframe and microcomputer versions, from project scoping, data collection and temperature study performance, to computer analysis, calibration, simulation, gaming and results interpretation and negotiation.  TRPA is currently marketing its own stream temperature modeling software.  The software, called StreamTemp: A Simple Network Stream

Temperature Model for Windows, is a stream temperature model for predicting changes in water temperature from upstream modifications in flow. Running in Microsoft Windows, it is a full extension of the SSSOLAR, SSSHADE and SSTEMP models developed by the U. S. Fish and Wildlife Service.


Acoustic Doppler Flow Measurements (ADCP) - TRPA has extensive experience conducting ADCP measurements for discharge and IFIM data collection in many rivers.  With two jet boats of different sizes, ADCP sampling can be conducted in many locations.  TRPA has also developed a mobile tether system for data collection in remote locations where no boat access exists and wading is not an option.  ADCP data allows for economical collection of the high volume field data required in many of today’s rigorous Instream Flow Studies.  TRPA has also developed a software program for importing ADCP data into RHABSIM.


ADCP Deployment with the Mobile Tether System and ADCP Cross-Section Profile.


Fishery Evaluations  - Fish habitat quality and utilization surveys, fish population estimates, spawning ground surveys, creel survey studies, fish age and growth studies, and project impact analyses have all been conducted by TRPA to evaluate potential impacts of existing and proposed development projects.


Bull Trout and Chinook Salmon

Aquatic Invertebrate Investigations  - TRPA has conducted a variety of aquatic invertebrate abundance and diversity studies in both freshwater and marine environments.  TRPA staff has been trained in the current rapid bioassessment techniques, including the California Aquatic Bioassessment Methodology.           


Hydrologic and Sediment Analysis  - In addition to routinely incorporating hydrologic analyses into instream flow studies and habitat studies, TRPA has evaluated sediment transport and deposition both within stream systems and on deltas formed at the confluence of small tributaries and major rivers.


Licensing Document Preparation  - Fisheries sections of licensing and re-licensing documents such as environmental impact assessments, applications to FERC, and special use permits have been prepared by TRPA to satisfy regulatory requirements. 


Project Review and Expert Testimony  - TRPA has been retained on numerous occasions to review previously conducted instream flow studies and project designs, provide an independent evaluation, and participate in State and Federal proceedings as an expert witness involving disputes over study conduct, the potential for project impacts, and required mitigation.


Fish Passage and Migration Barrier Evaluations – TRPA has performed a number of anadromous fish barrier evaluations to assess potential passage enhancement alternatives, and has provided technical assistance with the design of fish ladders, both conventional (pool-and-weir, Alaskan, steep pass) and naturalized (embedded boulders with resting pools).



Projects involving water issues in Western states have included:


·         Upper North Fork Feather River Hydroelectric Project Relicensing.  Pacific Gas and Electric Company.  Project relicensing activities include application of IFIM to the North Fork Feather River and Butt Creek, collecting habitat suitability criteria data for several species of fish, evaluation of trout spawning in project area, and water temperature modeling. 

·         Lower Putah Creek Fish Investigations.  Solano County water Agency.  Have conducted long term fish population studies on this Sacramento River tributary including semi-annual electrofishing surveys and larval fish surveys using daytime dipnet sampling and nighttime drift net sampling, and recreational angler surveys.          

·         Snake River Basin Water Rights Adjudication.  Idaho State Attorney General.  Claims made by Federal and Tribal agencies for State water rights are currently being evaluated by TRPA through a program of office review and field studies on numerous major rivers and streams tributary to the Snake River in Idaho.  Claims are based in part on approximately 1,300 instream flow studies conducted by the US Forest Service and on behalf of Indian tribes.  Work includes development of new species criteria curves applicable to large, medium, and small streams and expert witness testimony.

·         Middle Fork and South Fork Stanislaus River Instream Flow Study.  Pacific Gas and Electric Company.  Instream flow needs for resident trout were evaluated as part of project relicensing for the Spring Gap-Stanislaus Project.  The study included habitat mapping, hydraulic modeling, habitat modeling, and species criteria curve development in both the Relief and Sand Bar Diversion Dam Bypass reaches of the Middle Fork and in the South Fork Stanislaus River between Pinecrest and Lyons reservoirs.

·         Bucks Creek Instream Flow Studies.  Pacific Gas and Electric Company.  Instream flow impacts of a proposed expansion of an existing hydroelectric project were studied by TRPA on the Bucks Creek system.  The development presently contains three storage reservoirs, interbasin water transfers, and two powerhouses, and an additional powerhouse was proposed.  Instream flow analysis was conducted on Milk Ranch, Bucks, and Grizzly Creeks using new site-specific criteria curves for rainbow trout to determine the basis for negotiated flow releases from the project.

·         Yakima River Fisheries Investigations.  Yakima Coalition of Irrigation Districts.  TRPA participates in a quality control review of a major instream flow study to assess flow needs in the Yakima River basin.  The Yakima River contains several storage reservoirs and is almost entirely controlled for irrigation diversions and agriculture.  Studies conducted by TRPA include reanalysis of instream flow field data, habitat mapping of 230 river miles, creation of site-specific species criteria curves for spring Chinook salmon, collection of supplemental instream flow field data, examination of basin temperature alterations, water temperature modeling, and instream flow recommendations.




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