In the fall of 1999 the lobster population of western Long Island Sound (WLIS) experienced a massive die-off (LoBue et al. 2003). In fact, the lobster populations in WLIS still have not recovered as of this writing (Benway et al. 2004). Factors suspected of playing roles in this mortality event include water temperature, hypoxia and a neoparameoba. The overall objective of this study is to obtain an understanding of bottom water chemical conditions in WLIS, and their potential influence on benthic community structure and lobster health. Beginning in May 2002, water samples were collected within 5.0 cm and at 1.0 m above the bottom at 12 selected stations in WLIS and analyzed for dissolved NH4, H2S and O2. Grab samples for benthic community determination and sediment-profile images were simultaneously obtained with the water samples at 6 of the 12 stations. The data collected provide an accurate field record of the apparent levels of dissolved oxygen in the sediments of western Long Island Sound, as reflected in apparent redox depths (as recorded in sediment-profile images) and the amount of ammonia, hydrogen sulfide and oxygen present in the bottom waters, over a period critical to the LIS lobster fishery. Levels of dissolved oxygen in actual (within 5 cm) bottom waters of WLIS remain low throughout the summer and fall, despite the increase in dissolved oxygen recorded in the fall in waters 1 m above the bottom. Dissolved sulfide and ammonia concentrations in bottom waters of WLIS increased during spring and fall. These chemicals have been shown by other researchers to be physiologic stressors on lobsters and other marine life that live within benthic environments (Knezovich et al. 1996, Lianso 1991, McMahon & Wilkens 1975, Shumway & Scott 1983, Theede et al. 1969, Vargo & Sastry 1978, Vismann 1990, Wang & Widdows 1991). Given that the lobster die-off of 1999 began in late summer to early fall, it is hypothesized that ammonia and sulfide released from the sediments during that time may have played a role in weakening the lobsters. A comparison of water quality and temperature data from this study with that collected by the CT DEP at certain stations in WLIS during 1999 revealed some similarities and further strengthens the argument that environmental stressors played a role in the lobster mortality event of 1999.