The diked and freshened Herring River estuary (Wellfleet, Massachusetts) experiences regular summer hypoxia and one- to three-week periods of main stream anoxia, often accompanied by fish kills. Stream hypoxia results from the temperature-dependent increase in oxygen demand of organic matter released by diked salt marsh deposits; periods of total anoxial are induced by heavy rains which increase the runoff of wetland organic matter. Historic reductions in tidal flushing have extended the low salinity region of the estuary normally characterized by high organic loads and minimal flushing. Recurrent main stream anoxia has depressed both migratory and resident aquatic fauna.