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This three year study was designed to characterize benthic communities (macroinvertebrates) and physical habitat annually in two urban stream areas (Arcade Creek and Salinas streams) in California. Concurrent water quality evaluations, physical sediment parameters, pyrethroids, and bulk metals [including simultaneously extracted metals (SEM) and acid volatile sulfides (AVS) ratios] were also measured in both study areas. The relationship of various benthic metrics to physical habitat metrics, pyrethroids, and metals was evaluated for the the three year data set (2009 -2011) using univariate analysis, stepwise multiple regression analysis and canonical correlation analysis. Habitat conditions were determined to be poor in Arcade Creek and extremely poor in the Salinas streams.