Sediment denitrification is a microbial process that converts dissolved inorganic nitrogen in sediment porewaters to N2 gas, which is subsequently lost to the atmosphere. In coastal waters, it represents a potentially important loss pathway for fixed nitrogen which might otherwise be available to primary producers. Currently, data are lacking to adequately assess the role of denitrification in reducing or remediating the effects of large anthropogenic nitrogen loads to the coastal zone. This study describes the results of 88 individual measurements of denitrification (as a direct flux of N2 gas) in sediment cores taken over a 3-yr period (1991-1994) from six stations in Boston Harbor, nine stations in Massachusetts Bay, and two stations in Cape Cod Bay. The dataset is unique in its extensive spatial and temporal coverage and includes the first direct measurements of denitrification for North Atlantic shelf sediments. Results showed that rates of denitrification were significantly higher in Boston Harbor (mean = 54, range < 5-206 μmol N2 m-2 h-1) than in Massachusetts Bay (mean = 23, range < 5-64 μmol N2 m-2 h-1). Highest rates occurred in areas with organic-rich sediments in the harbor, with slower rates observed for low-organic sandy sediments in the harbor and at shallow shelf stations in the bay. Lowest rates were found at the deepest shelf stations, located in Stellwagen Basin in Massachusetts Bay. Observed rates were correlated with temperature, sediment carbon content, anti benthic macrofaunal activity. Seasonally, highest denitrification rates occurred in the summer in Boston Harbor and in the spring and fall in Massachusetts Bay, coincident with peak phytoplankton blooms in the overlying water column. Despite the fact that sediment denitrification rates were high relative to rates reported for other East Coast estuaries, denitrification losses accounted for only 8% of the annual total nitrogen load to Boston Harbor, a consequence perhaps, of the short water-residence times (210 d) of the harbor.