Urban land use alters channel morphometry, particle size structure, and sediment-transport dynamics in stream ecosystems, thereby degrading the habitat of aquatic organisms. However, stream form varies substantially among geoclimatic settings, and, thus, the degree of negative effects induced by urbanization may be region-specific. Biota in streams of the Coastal Plain ecoregion of the eastern US consistently show greater tolerance to urban land use than do biota of the adjacent Piedmont, potentially because of a disparity in geomorphic degradation between ecoregions. We quantified channel morphometry, particle mobility, sediment deposition, and floodwater chemistry in similarly sized rural and urban streams of both ecoregions to detect differences in urbanization-induced geomorphic change. Macroinvertebrate rates of recolonization in patches of disturbed benthic habitat also were monitored. No differences in channel morphometry were observed among treatment groups. Riffle particle sizes were significantly larger in urban than in rural Piedmont streams, but a corresponding disparity was absent in Coastal Plain streams. Particle mobility increased in urban settings uniformly between ecoregions. However, transported particles were substantially larger in Piedmont streams. Sediment deposition was higher overall in Coastal Plain streams but more affected by urbanization in Piedmont streams. Macroinvertebrate density in the disturbed habitat rose faster over time in Coastal Plain than in Piedmont streams. Results suggest that geomorphic degradation is greater in Piedmont streams and that organisms may be adapted to benthic instability in Coastal Plain streams. In addition, our findings demonstrate that ecosystem-scale responses of streams to urbanization may vary inherently among geoclimatic settings.