Bioassessment of the San Joaquin River: implications for chinook salmon habitat restoration

The San Joaquin River Restoration Program (SJRRP) is preparing to reintroduce threatened spring-run Chinook salmon (Oncorhynchus tshawytscha) into the San Joaquin River between Friant Dam near Fresno, California and the confluence of the Merced River. To assess river conditions, the SJRRP collected physical habitat and benthic macroinvertebrate data in 2010, 2011, and 2012 using the Surface Water Ambient Monitoring Program s Standard Operating Procedures for Collecting Benthic Macroinvertebrate Samples and Associated Physical and Chemical Data for Ambient Bioassessments in California. Preliminary analysis of the benthic macroinvertebrate results revealed that the San Joaquin River is in good biological condition only between Friant Dam and Gravelly Ford. I used this segment as a reference site and compared the habitat and benthic macroinvertebrate abundance and diversity to the other segments, and answered where restoration should occur and which habitat variables need to be restored for sustaining salmon. I used analysis of variance (ANOVA), Fisher s Least Significant Difference (LSD), and principal component analysis (PCA) to show that the San Joaquin River between Gravelly Ford and Mendota Dam and the Eastside Bypass and Merced River are in need of restoration. Restoration should focus on riparian vegetation complexity, percent gravel, and instream habitat complexity by adding boulders, woody debris, and artificial structures.