Human activities in urban areas can lead to both chemical pollution and physical alteration of stream habitats. The evaluation of ecological impacts on urban streams can be problematic where both types of degradation occur. Effects of contaminants, for example, may be masked if stream channelization, loss of riparian vegetation, or other physical stressors exert comparable or larger influences. In the Aberjona watershed (near Boston, MA, USA), we used physical, chemical, and biological indices to discern the relative impacts of physical and chemical stressors. We used standard protocols for assessing the biological condition of low-gradient streams, sampling macroinvertebrate communities from several different habitat types (e.g., overhanging bank vegetation, undercut bank roots, and vegetation on rocks). We strengthened the linkage between chemical exposure and macroinvertebrate response by measuring metal concentrations not only in sediments from the stream bottom but also in the vegetative habitats where the macroinvertebrates were sampled. Linear regression analysis indicated that biological condition was significantly dependent (95% confidence level) on contaminants in vegetative habitats, but not on contaminants in sediments from the stream bottom. Biological condition was also significantly dependent on physical habitat quality; regression analysis on both contaminants and physical quality yielded the best regression model (r2 = 0.49). Similar biological impairment was observed at sites with severe contamination or physical impairment or with moderate chemical and physical impairment. These results have implications for the management of urban streams.