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WSDOT Biological Assessment Guidance

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Biological Assessment Preparation for Transportation Projects - Advanced Training Manual - Version 2015

Part 1 - General Information for BA Authors

Part 2 - Guidance on Specific BA Topics

Part 3 - Additional Resources for BA Authors 

Stormwater Guidance

On February 16, 2009, the Federal Highway Administration (FHWA), National Marine Fisheries Service (NMFS), United States Fish & Wildlife Service (USFWS) and the Washington State Department of Transportation (WSDOT) signed a Memorandum of Agreement (MOA) (pdf 130 kb) committing these four agencies to use a common methodology for analyzing the effects of stormwater on Endangered Species Act (ESA)-listed fish species. The methodology includes the Western Washington Highway Runoff Dilution and Loading Stormwater Model (HI-RUN Model), its user guide, and accompanying stormwater assessment guidance that is posted below. A Stormwater Impact Assessment Chapter has been incorporated into Part 3 of the WSDOT Biological Assessment Preparation for Transportation, Advanced Training Manual.

The approach is required in all biological assessments submitted by WSDOT or WSDOT Local Programs. 

Note that there is a separate assessment process for Eastern Washington that does not involve the use of the HI-RUN model.  Also to Note, the HI-RUN Model User's Guide and Stormwater Chapter were all updates in January 2011.  Be sure you are using the most recent version.

Western Washington Stormwater Assessment Guidance

The HI-RUN Model should only be used for stormwater analysis associated with biological assessments, and should not be used as a design tool.

Examples for Using the HI-RUN Model

Endangered Species Act Stormwater Design Checklist for Western Washington (doc 162 kb) - January 2010

*Please download to your computer prior to use.  Please contact Marion Carey, if you encounter problems or errors when using the HI-RUN Model.

Eastern Washington Stormwater Guidance

Highway Runoff Manual Endangered Species Act Stormwater Design Checklist for Eastern Washington (doc 119 kb) - January 2010

Stormwater Whitepapers

Programmatic Stormwater Monitoring Approach

On October 30, 2009, WSDOT, FHWA, NOAA Fisheries and USFWs agreed to use a Programmatic Monitoring Approach for Highway Stormwater Runoff in Support of Endangered Species Act Section 7 Consultation in Washington State for Projects which result in “ may adversely effect” determinations on listed fish species due to the creation of new impervious surface that may result in water quality related effects to listed fish species. This approach focuses on utilizing the WSDOT NPDES permit monitoring requirements to meet stormwater monitoring needs rather than monitoring individual projects. The compiled data will be used to improve the accuracy and reliability of the current stormwater models. In addition to developing this programmatic monitoring approach, staff from WSDOT and the Services also developed standard terms and conditions that reference that approach. These terms and conditions are contained in the agreement.

FHWA funded local agency projects that are similar in scope to WSDOT projects and meet or exceed the requirements of the Highway Runoff Manual for stormwater treatment may also be able to utilize this approach.

There is no phase-in timeline for using this approach. It should be applied to any project which has utilized the HI-RUN Model as part of their stormwater analysis.


Indirect Effects Stormwater Runoff Analytical Method

On April 14, 2011, WSDOT, FHWA, NOAA Fisheries , USFWS and WSDOT signed a MOA committing these four agencies to use the Indirect Effects Stormwater Runoff Analytical Method in consultations which have development identified as in indirect effect of a transportation project. This analytical method is intended to evaluate water quality impacts associated with stormwater runoff from development identified as an indirect effect of transportation projects The method serves as an addition to the guidance issued on June 17, 2009 titled Endangered Species Act (ESA), Transportation and Development; Assessing Indirect Effects in Biological Assessments. All WSDOT BAs submitted after June 14, 2011 and all Local agency projects submitted after October 14, 2011 are required to use this method for analyzing the water quality impacts associated with stormwater runoff associated with development identified as an indirect effect of transportation projects.

Noise Assessment Guidance


The tables below provide summary information on marine mammal, fish, and marbled murrelet injury and disturbance thresholds for impact pile driving, and estimated auditory bandwidths (estimated hearing frequency ranges) for marine mammals and fish.

On November 19, 2013, WSDOT hosted a USFWS presentation that introduced marbled murrelet in-air noise masking guidance for marine water pile driving projects.  The supporting white paper is anticipated to be released by the USFWS in the near future.  The USFWS is using this guidance in marine pile driving consultations.


An Hydroacoustic Workshop addressing the fish noise exposure criteria was held on August 11, 2008. The National Marine Fisheries Service's provided a calculator for calculating the distance to the new thresholds for fish. 

USFWS has created an excel spreadsheet calculator that assists in determining when and to what distance sound pressure levels generated by impact pile driving projects exceed the thresholds.

Pile Driving Information 

The tables below provide information on the typical number of pile strikes for steel piles, peak sound pressure levels and sound exposure levels for various sizes and types of piles. The data in these tables can be used to estimate sound pressure and cumulative sound exposure levels (SELcum) for various pile diameters and types. WSDOT Pile driving monitoring reports can help with site specific information for projects in the same or similar areas. The link to the CalTrans Pile Driving Compendium is also provided for comparison.


On February 28, 2012, WSDOT, FHWA, and USFWS signed a MOA agreeing to use new criteria that identify the onset of injury to marbled murrelets from underwater sound pressure levels associated with impact pile driving. All WSDOT and local agency BAs submitted after April 28, 2012 are required to use these new criteria.

As a result of a multi-agency agreement (pdf 793 kb), fish noise exposure interim criteria was implemented beginning October 1, 2008. All WSDOT projects with pile driving activities that may impact fish are required to use this criteria when assessing potential impacts to fish.

Research Documents

Additional Acoustical Resources


Terrestrial Noise Assessment

Use the information in Chapter 7 of the BA Preparation for Transportation Projects Advance Training manual to help determine the appropriate decibel levels for ambient noise, traffic noise and construction noise.

Marbled Murrelet and Spotted Owl Guidance

The U.S. Fish and Wildlife Service (USFWS) has redefined the marbled murrelet nesting season. In brief, the nesting season has been extended for one week, and it is no longer divided into an early and late season, but is considered a single season. Using data from 137 nests from southern British Columbia to northern Oregon, the nesting season of marbled murrelets in Washington is defined as the period from April 1 to September 23 (the previously defined nesting season was April 1 to September 15). USFWS will still be applying the limited operating period (LOP) of two hours after sunrise to two hours before sunset to facilitate murrelet protection during the nesting season.

After September 4, the potential to encounter a murrelet during the implementation of a single action may be extremely low.  It may therefore be feasible, with implementation of an LOP, to justify that the risk of exposure of murrelets is discountable after September 4. Factors that could support a discountable determination during this time period include low quality habitat, and type and duration of activity. In short, proposed construction after September 4 with an LOP in effect will not automatically result in a Not Likely to Adversely Affect (NLTAA) determination.

They implemented this new definition in 2013.  In 2012, the USFWS implemented a definition of marbled murrelet nesting habitat based on the presence of potential nest platforms. All BAs that are submitted to the USFWS must use these new definitions.

In 2015, the USFWS issued a programmatic Biological Opinion for WSDOT activities. The BO establishes harassment/injury distances for noise-generating activities specific to marbled murrelets and northern spotted owls that replaces the 92 dBA threshold with the distance thresholds. The standard threshold distances described in the BO can be used as a tool to assist the biologist in making effect determinations on typical transportation projects.

It is important to note that the BO is only applicable for use in certain situations because it was developed for a specific program of activities. The threshold and effect distances were determined after factoring a suite of activities and minimization measures specific to the project. The following appendices to the BO are relevant to marbled murrelets and northern spotted owls.

Indirect Effects Guidance

On June 17, 2009, the USFWS, NOAA Fisheries Service, FHWA and WSDOT entered into an agreement to use the 2009 Indirect Effects Guidance in the completion of biological assessments. All WSDOT projects are required to use this guidance.

This 2009 Indirect Effects Guidance supersedes the previous version of the guidance (2003 Indirect Effects Guidance).

Consulting on Listed Plants

WSDOT has developed this brief guidance  (pdf 27 kb) to facilitate consultations related to listed plants. For help on identification of plant species and their habitats, the Washington State Department of Natural Resources' Natural Heritage Program and the Spokane District of the U.S.D.I. Bureau of Land Management prepared a Field Guide to Selected Rare Plants of Washington

Marine Mammal ESA Consultations

The National Marine Fisheries Service Marine Mammals Section 7 Consultation tools explain the relationship between the Endangered Species Act and the Marine Mammal Protection Act, effects of noise on marine mammals, sound threshold guidance, and other related topics.