Summertime hypoxia regularly occurs in the bottom waters of Smithtown Bay, Long Island Sound. Hypoxia, defined in this study as <3.0 mg O2 L-1, is plaguing many of our coastal estuaries and can be detrimental to aquatic organisms. A generally accepted model for the cause of coastal hypoxia in temperate regions is the establishment of seasonal water column stratification and the introduction of anthropogenic nutrients from sewage treatment plants, combined sewer overflows, agricultural fertilizers, urban runoff, sediment remineralization, and atmospheric deposition. However, there are no major point sources of anthropogenic nitrogen that discharge directly into Smithtown Bay. Despite great efforts to reduce nitrogen loading into Long Island Sound, summertime hypoxia is a continuing occurrence in Smithtown Bay. While hypoxic conditions remain seasonally prevalent in the bay, the surrounding bottom waters have considerably higher concentrations of dissolved oxygen. This study examines the causes of hypoxia in Smithtown Bay and how the problem is more complex than the introduction of anthropogenic nitrogen. Strong, thermally controlled stratification and mid-depth pycnoclines inhibit vertical mixing and the replenishment of dissolved oxygen to bottom waters. The two headlands, Crane Neck and Eatons Neck, may be creating a partial boundary between the bay and the rest of the Sound, preventing lateral mixing. This results in weak currents and bottom stress and a limited exchange of water masses over a tidal cycle. Furthermore, the classical headland gyre setting may increase the residence time of suspended particulate material transported from land into Smithtown Bay. The trapped particulate material inside the bay will sink and increase the consumption of bottom water dissolved oxygen. It appears, from these results, that Smithtown Bay is physically predisposed to hypoxia. For this reason, it is likely that the current management solution to hypoxia of implementing total maximum daily loads of nitrogen will not alleviate the hypoxia problem in Smithtown Bay.