The chemical and biological impacts of anthropogenic physical modifications (i.e., channelization, dredging, bulkhead, and jetty construction) to tributaries were assessed on New York’s Long Island South Shore Estuary. Water-quality data collected on Carmans, Patchogue, and Swan Rivers from 1997 to 2005 indicate no significant differences in nutrient levels, temperature, or pH among the rivers, but significant differences in light transmittance, dissolved oxygen (DO), salinity, and sediments were observed. Patchogue River (PR) and Swan River (SR) were significantly more saline than Carmans River (CR), PR and SR had less light transmittance than CR, and both exhibited severe warm season hypoxia. CR was rarely hypoxic and only at the lower layer of the deepest station in warm seasons. Deep stations on PR had hypoxic readings year round, but the shallower SR was well-oxygenated at all stations after the fall turnover. There were wide diel and seasonal variations in chlorophyll a on each river, and measurements were significantly higher at poorly flushed stations. In warm seasons, this often resulted in hyperventilation with supersaturated DO in the upper water column on sunny days, and suboxic conditions at nights and/or in deeper layers. PR sediments were anoxic, SR sediments ranged from normal to anoxic, and CR sediments were normal at all stations. Polyaromatic hydrocarbon concentrations in PR sediments were over three orders of magnitude higher than SR and CR sediments. Benthic invertebrate assessment of species richness, biotic index, and Ephemeroptera, Plecoptera and Trichoptera richness indicated that PR was severely impacted, SR ranged from slightly to severely impacted, and CR ranged from non-impacted to slightly impacted. Diversity and abundance of plankton were comparable on SR and CR, and were significantly higher than on PR. The data indicate that nutrients do not play a major role in hypoxia in these estuarine tributaries but that physical forces dominate. The narrow inlets, channelization, and abrupt changes in depth near the inlets of PR and SR foster hypoxic conditions by inducing salinity stratification that limits vertical mixing and by restricting horizontal water mass exchange with the bay. The study suggests that other tributaries with such physical modifications should be examined to assess the temporal and spatial extent of hypoxia.