Assessment of Salmonids and Their Habitat Conditions in the Walla Walla River Basin within Washington: 2006 Annual Report

This study began in 1998 to assess salmonid distribution, relative abundance, genetic characteristics (stock status and trends), and the condition of salmonid habitats in the Walla Walla River Subbasin within Washington.

Stream flows in the Walla Walla Subbasin continue to show a general trend that consists of a decline in discharge in late May or June, followed by low summer flows and usually an increase in discharge in fall, or later in winter. Stream flows in the mainstem Walla Walla River have shown substantial increases in some areas in recent years. The increase is apparently associated with a 2000 settlement agreement between the U.S. Fish and Wildlife Service (USFWS) and the Irrigation Districts to leave minimum flows in the Walla Walla River. We documented low flows in the fall in the mainstem Walla Walla River that are far below the settlement agreement flows. The low flows we documented of less than 15 cfs likely create a severe limitation on salmonid survival, migration or use of this portion of the river. Additional emphasis needs to be placed on maintaining adequate stream flows in the fall, in addition to during summer and late spring.

Stream temperatures in 2006 in the Walla Walla Subbasin were similar to those in 2005. Upper montane tributaries maintained maximum summer temperatures below 65°F, while sites in the middle and lower Touchet and Walla Walla rivers frequently had daily maximum temperatures well above 68°F (high enough to inhibit migration in adult and juvenile salmonids, and to sharply reduce survival of their embryos and fry). We summarized the water temperature data for several sites in the lower reaches of the Walla Walla River, Mill Creek, Dry Creek and the Touchet River and compared seven day maximum temperatures with thermal criteria for unimpeded fish passage. We identified many sites and years with apparent thermal passage impediments in the lower portions of each of these stream systems. High temperature is possibly the most critical physiological barrier to salmonids in the Walla Walla Subbasin, but other factors (available water, turbidity or sediment deposition, cover, lack of pools, etc.) also affect salmonid distribution, survival, migration, and breeding success. Increased flows in the Walla Walla River from the USFWS/Irrigation Districts settlement agreement have not produced consistent improvements to water temperatures in the settlement area within Washington, or to stream flows and water temperatures downstream.

Rainbow/steelhead trout (Oncorhynchus mykiss) represent the most common salmonid in the subbasin. Other salmonids including; bull trout (Salvelinus confluentus), chinook salmon (Oncorhynchus tshawytscha), and mountain whitefish (Prosopium williamsoni) had low densities and limited distribution throughout the subbasin. We began a detailed review of all the fish sampling data WDFW has available from several hundred sites since 1997 to examine distribution of rainbow/steelhead, whitefish, bull trout, chinook, brown trout and lamprey. The data summary provides an evaluation by stream reach of distribution and relative abundance for these species. All these species, except rainbow/steelhead, have fairly limited distribution within the Washington portion of the basin. Rainbow/steelhead have widespread distribution, although they are absent during summer in some of the portions of headwater areas and in the lower reaches of the basin where water temperatures are high.

Steelhead spawning surveys were conducted in four streams in the Walla Walla Subbasin in 2006. Surveyors found 46 redds on Mill Creek and only 9 redds in the Coppei Creek system (both South Fork and mainstem) and none in Yellowhawk Creek. Survey conditions were poor with high flows and turbid conditions during the first part of the spawning season. Therefore, the steelhead spawning surveys should be considered as minimum estimates. Bull trout spawning surveys in the upper Touchet River tributaries found a total of 46 redds and 12 live fish, which is a substantial decrease from the previous year (74 redds and 51 live fish). We did not survey any more than the Wolf Fork and North Fork in 2006, and surveys began later than usual because of the approximately 110,000 acre Columbia Complex Fire and associated access restrictions. Spring chinook spawning surveys were not conducted in portions of the Touchet River in 2006, because few adults were observed at the adult trap in Dayton, and no redds or adults were observed during bull trout spawning surveys.

After many years of collecting tissues from steelhead and bull trout, WDFW completed genetic characterizations using microsatellite DNA analyses for steelhead (as well as in the Tucannon River and at Lyons Ferry Hatchery) and bull trout in the Walla Walla Basin. Results of the steelhead analysis indicate that steelhead are quite genetically different in the Walla Walla and Touchet Basins and that there is little evidence to suggest hatchery introgression into the natural populations in the Walla Walla Basin. Results of the bull trout analysis show statistically significant genetic differences among migratory bull trout in the Walla Walla River near Milton- Freewater, upper Mill Creek and the Touchet River at Dayton. In addition, significant genetic differences were found for juvenile bull trout collected from five spawning areas of the upper Touchet River drainage.

Recommendations for assessment activities in 2007 include:

1) Monitor habitat conditions to develop an adequate baseline, improve values in the Ecosystem Diagnosis and Treatment (EDT) model, and to monitor changes that result from habitat improvements.

2) Continue bull trout and steelhead spawning surveys, and emphasize improving counts or estimates of returning adults to determine escapement annually at key locations within the subbasin.

3) Continue, and expand the compilation of fish distribution and relative abundance for fish or other aquatic species, including other data sets from CTUIR and others, as well as incorporation of GIS mapping of distribution and abundance.

4) Identify appropriate management units for bull trout based on genetic information available from this project, and determine causes for declines of bull trout in the Touchet River to prevent extirpation of these groups of salmonids.

5) Work with other managers in the Walla Walla Subbasin to compile fish and habitat data to fill gaps, improve planning, and evaluate efforts to restore salmonids in the subbasin.

6) Continue to work with CTUIR and others to develop a comprehensive RM&E plan for the subbasin.