Hood Canal is a long (110 kilometers), deep (175 meters) and narrow (2 to 4 kilometers wide) fjord of Puget Sound in western Washington. The stratification of a less dense, fresh upper layer of the water column causes the cold, saltier lower layer of the water column to be isolated from the atmosphere in the late summer and autumn, which limits reaeration of the lower layer. In the upper layer of Hood Canal, the production of organic matter that settles and consumes dissolved oxygen in the lower layer appears to be limited by the load of dissolved inorganic nitrogen (DIN): nitrate, nitrite, and ammonia. Freshwater and saline loads of DIN to Hood Canal were estimated from available historical data. The freshwater load of DIN to the upper layer of Hood Canal, which could be taken up by phytoplankton, came mostly from surface and ground water from subbasins, which accounts for 92 percent of total load of DIN to the upper layer of Hood Canal. Although DIN in rain falling on land surfaces amounts to about one-half of the DIN entering Hood Canal from subbasins, rain falling directly on the surface of marine waters contributed only 4 percent of the load to the upper layer. Point-source discharges and subsurface flow from shallow shoreline septic systems contributed less than 4 percent of the DIN load to the upper layer. DIN in saline water flowing over the sill into Hood Canal from Admiralty Inlet was at least 17 times the total load to the upper layer of Hood Canal. In September and October 2004, field data were collected to estimate DIN loads to Lynch Cove - the most inland marine waters of Hood Canal that routinely contain low dissolved-oxygen waters. Based on measured streamflow and DIN concentrations, surface discharge was estimated to have contributed about one-fourth of DIN loads to the upper layer of Lynch Cove. Ground-water flow from subbasins was estimated to have contributed about one-half of total DIN loads to the upper layer. In autumn 2004, the relative contribution of DIN from shallow shoreline septic systems to the upper layer was higher in Lynch Cove (23 percent) than in the entire Hood Canal. Net transport of DIN into Lynch Cove by marine currents was measured during August and October 2004-a time of high biological productivity. The net transport of lower-layer water into Lynch Cove was significantly diminished relative to the flow entering Hood Canal at its entrance. Even though the net transport of saline water into the lower layer of Lynch Cove was only 119 cubic meters per second, estuarine currents between 33 and 47 m were estimated to have carried more than 35 times the total freshwater load of DIN to the upper layer from surface and ground water, shallow shoreline septic systems, and direct atmospheric rainfall. The subsurface maximums in measured turbidity, chlorophyll a, particulate organic carbon, and particulate organic nitrogen strongly suggest that the upward mixing of nitrate-rich deeper water is a limiting factor in supplying DIN to the upper layer that enhances marine productivity in Lynch Cove. The presence of phosphate in the upper layer in the absence of dissolved inorganic nitrogen also suggests that the biological productivity that leads to low dissolved-oxygen concentrations in the lower layer of Lynch Cove is limited by the supply of nitrogen rather than by phosphate loads. Although the near-shore zones of the shallow parts of Lynch Cove were sampled, a biogeochemical signal from terrestrial nitrogen was not found. Reversals in the normal estuarine circulation suggest that if the relative importance of the DIN load of freshwater terrestrial and atmospheric sources and the DIN load from transport of saline water by the estuarine circulation in controlling dissolved-oxygen concentrations in Lynch Cove is to be better understood, then the physical forces driving Hood Canal circulation must be better defined.