Development of seasonal hypoxia was studied weekly in the western narrows of Long Island Sound (WLIS) during the summers of 1992 and 1993 by measuring hydrographic properties, biological oxygen demand (BOD), biomass, production, and mortality of phytoplankton and bacterioplankton in the water column. Dissolved oxygen in bottom waters was low and variable during stratified periods (19–51% saturation), oscillating in and out of hypoxic conditions (defined as <3 mg O₂ l⁻¹ or 94 μM O₂). Hypoxia was more prevalent in 1993 than in 1992, corresponding to greater water column stratification in 1993. Microbial BOD in bottom waters appeared to be fueled by delivery of autochthonous carbon from phytoplankton blooms rather than allochthonous carbon input. Phytoplankton production responded to elevated NH₄ ⁺ concentrations, especially when the mixed layer was shallow. NH₄ ⁺ concentrations generally varied as a function of the preceding week's rainfall (r²=0.765). Bacterial production did not covary with phytoplankton production, yet was closely correlated with particulate organic carbon, which was chlorophyll-rich. Results indicate that the timing and severity of hypoxia development are strongly coupled to allochthonous input of NH₄⁺ after heavy precipitation. Observations illustrate for the first time that bottom waters in this system oscillate in and out of hypoxia on an almost weekly basis rather than sustain them over the entire stratified period. The frequency of these oscillations depends upon variations in nutrients, planktonic production and export, and bottom water ventilation.