Some key findings:

1. Biotic conditions, as measured by the California Stream Condition Index (CSCI), were best in the upper watershed and worst in the lower watershed, where lined and altered stream channels predominate. CSCI scores at 70% of sites in the watershed were below levels associated with reference condition. Communities in the upper watershed were characterized by organisms that were pollution sensitive and exhibited a wide range of feeding strategies. In contrast, the lower watershed was dominated by more tolerant organisms employing only a few feeding strategies.
2. Riparian zone physical habitat conditions ranged from nearly pristine in the upper watershed to moderately to highly degraded in the channelized lower tributaries and mainstem, respectively, as measured by the California Rapid Assessment Method (CRAM). Similarly, physical habitat conditions as measured by SWAMP followed this same pattern.
3. Nutrients and metals were consistently lower at upper watershed sites compared to the lower tributaries and mainstem. Nutrients were greatest on the mainstem, while most metals were greatest in the lower tributaries. An exception to this was zinc which was much greater on the mainstem compared to the other sub-regions.
4. There were few exceedances of dry weather Basin Plan standards for any water quality parameters measured during the period. Nitrate and ammonia were well below the thresholds and there were no exceedances of the hardness adjusted CTR for any dissolved metal.
5. When measured, organophosphorus pesticides and pyrethroids were nearly always below method detection limits.
6. Of the total of 71 toxicity tests (142 endpoints) conducted since 2009 , only five samples were identified as toxic. Significant survival effects were observed in a single test in 2010, while four tests exhibited only reproductive effects in 2011, 2012 and 2013, all in the lower watershed. No acute or chronic toxicity was measured from eight samples collected in 2014. In 2017, toxicity testing of stream water was dropped by the TSG due to the low frequency of toxic events.
7. There was a strong relationship between the condition of the biological community and physical habitat conditions. Sites in the lower watershed were characterized by concrete lined channels, increased nutrients (nitrate and ammonia) and zinc. Conversely, sites in the upper watershed had good epifaunal cover, and increased amounts of cobble and canopy cover. There was also clear separation by biotic condition, with the best CSCI scores in the upper watershed and the poorest in the lower tributaries and mainstem channel.
8. Environmental variables shown to be most closely associated with patterns in the biotic condition included chloride, physical habitat condition (epifaunal substrate and channel alteration) and sulfate.