Multivariate spatial patterns of 38 environmental variables (habitat metrics, metals, pyrethroids and sediment characteristics) and 14 benthic metrics were determined from over a decade of sampling in five California waterbodies. Canonical discriminant analyses produced very highly significant separations of the five watersheds based on environmental variables. The discriminant analyses based on benthic metrics also produced highly significant separations, although confidence ellipses were not quite as well separated as the environmental variables. Separation of creeks made ecological sense as Pleasant Grove Creek (PGC), which appeared to have greater habitat quality also had benthic metrics indicative of less stressed benthic communities, while the Santa Maria River watershed (SM) appeared to have lower habitat quality and more toxicants in the sediments also appeared to have benthic communities indicative of stress-tolerant taxa. The benthic community health of the other three creeks (Arcade Creek [ARC], Kirker Creek [KC] and Salinas Streams [SAL]) were considered intermediate in apparent stress between PGC and SM. Overall, benthic communities were somewhat more similar between creeks than were the environmental conditions. Benthic communities have greater overlap in characteristics than would be expected from environmental conditions, perhaps due to a greater resilience since they are generally dominated by tolerant benthic taxa.