Streamflow is a primary driver of river and stream ecology. Lotic organisms are adapted to living in flowing water with a characteristic timing, duration, and magnitude of high and low flow events. Alteration of this flow regime as a result of impoundments, water withdrawals, and changes to land use patterns is frequently accompanied by dramatic changes to the biotic assemblages. We investigated effects of flow alteration on stream ecology in the Sudbury River, a river located in a suburban Boston and that has long been exploited for water resources. The Sudbury River has the full complement of flow alterations, including: mainstem impoundments, surface and groundwater withdrawals, and urbanization. Analysis of 33 years of stream gage data indicates that the river is undergoing contemporary hydrologic alteration. These changes include a roughly 200% increase in rise rates of flows, an approximate 65% decrease in 1-day minimum flows, and a trend towards increasing high flow pulse counts. Biotic sampling of macroinvertebrates, mussels, and fishes in summer of 2014 demonstrated that the Sudbury River is now dominated by generalist species. The high proportion of tolerant and moderately tolerant macroinvertebrate taxa within our samples suggests that water quality pollution is a problem in the Sudbury. Of five mussel species sampled, all are generalists in their habitat requirements. Though one mussel species of special concern was sampled, the most abundant species collected were the widespread Eastern elliptio (58%) and Eastern lampmussel (40%). We used the target fish community (TFC) model to assess the degree to which the fish assemblage deviated from that expected for a river with similar zoogeographic and physical features. Overall, the current community has a 22.7% similarity to the TFC. Of the four fluvial specialist species present in the TFC, only fallfish was sampled in our study. The fish assemblage has shifted from one that should be dominated by fluvial specialist and fluvial dependent species to one overwhelmingly dominated by macrohabitat generalists (90.6% of fishes sampled). These shifts in biotic assemblages are consistent with other studies that show shifts in assemblages from fluvial specialists to habitat generalists with hydrologic alteration. If the current trends continue, it is likely that biotic assemblages will experience increasing pressure from hydrologic alteration.