We examined the accumulation of manganese (Mn) in gill tissues of chemically naïve lobsters held in situ at six sites in Long Island Sound (LIS) for up to six weeks to evaluate the possible contribution of eutrophication-driven habitat quality factors to the 1999 mass mortality of American lobsters (Homarus americanus). These western LIS lobster habitats experience seasonal hypoxia, which results in redox-mobilized Mn being transferred to and deposited on the tissues of the lobsters. Manganese accumulated in gill tissue of lobsters throughout the study, but rates were highest at western and southern LIS sites, ranging from 3.4–0.8 μ g/g/d (~16 μg/g initial). The Baden-Eriksson observation that Mn accumulation in Norway lobsters (Nephrops norvegicus) is associated with ecosystem hypoxia is confirmed and extended to H. americanus. It seems likely that, after accounting for molting frequency, certain critical values may be applied to other lobster habitats of the NE US shelf. If a high proportion of lobsters in autumn have gill Mn concentrations exceeding 30 μg/g, then the habitats are likely experiencing some reduced oxygen levels. Manganese concentrations above 100 μg/g suggest exposure to conditions with the potential for lobster mortality should the temperatures of bottom waters become elevated, and gill concentrations above some higher level (perhaps 300 μg/g) indicate the most severe habitat conditions with a strong potential for hypoxia stress.