In a longitudinal study of two streams whose lower reaches received unattenuated urban stormwater runoff, physical disturbance by stormflow was less important than the persistant unidentified chemical impacts of urban stormwater in limiting the distribution of Chironomidae, and Ephemeroptera, Trichoptera and Plecoptera (EPT). A hierarchical spatial analysis showed that chironomid density did not decrease from rural to urban stream reaches. Instead, the taxonomic composition of chironomid assemblages was significantly altered in urban versus rural reaches; chironomid assemblages in urban reaches exhibited higher average pollution tolerance scores. In contrast, the density of EPT was significantly lower in urban reaches. Despite higher values of stormflow tractive force in urban reaches, streambed stability tended to be greater in urban reaches. Modeling of temporal variation in chironomid density showed similar patterns in both rural and urban reaches: chironomid density had a unimodal relationship to rainfall index (RI), with highest densities at intermediate values of RI. Models of EPT density over time in rural reaches showed no significant relation to RI, and temporal variation in EPT density in urban reaches was not predictable. The abundance of fine particulate organic matter, including periphyton (FPOM), on cobbles was greater in urban reaches and showed a much greater degree of temporal variation than in rural reaches. In urban reaches, a negative relation between FPOM and RI indicated the importance of stormflow abrasion.