Human alteration of the stream environment can affect benthic communities in multiple ways. In urban areas, such as southern California, multiple stressors may impair streams simultaneously, as urbanization typically results in degradation of the physical habitat, poor water quality, and high toxicity to benthic organisms. In order to identify which stressors have the greatest impact, we analyzed a dataset of 38 sites from Orange County, California, which included pristine and heavily impaired streams. At each site, benthic invertebrates, water chemistry, and physical habitat data were measured; additionally, water and sediment toxicity was assayed. We evaluated the effects of physical habitat, water chemistry, and toxicity on macroinvertebrate community structure using univariate and multivariate methods. Partial constrained ordination showed that physical habitat variables explained the largest proportion of variability in community structure. For example, 7 physical habitat variables had strong (|ρ| > 0.2) Spearman rank correlations with ordination axes, whereas only 2 water chemistry variables did.  and  This research will help design future monitoring programs, as well as help set management and restoration priorities by determining which stressors have the greatest impacts on the ecological health of streams.