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Hood Canal, Washington, USA, is a poorly ventilated fjord-like sub-basin of Puget Sound that commonly experiences hypoxia. This study examined the influence of watershed soils, vegetation, physical features, and population density on nitrogen (N) export to Hood Canal from 43 tributaries. We also linked our watershed study to the estuary using a salinity mass balance model that calculated the relative magnitude of N loading to Hood Canal from watershed, direct precipitation, and marine sources. The overall flow-weighted total dissolved N (TDN) and particulate N input concentrations to Hood Canal were 152 and 49 μg l, respectively. Nitrate and dissolved organic N comprised 64 and 29% of TDN, respectively. The optimal regression models for TDN concentration and areal yield included a land cover term suggesting an effect of N-fixing red alder ( Alnus rubra) and a human population density term (suggesting onsite septic system (OSS) discharges). There was pronounced seasonality in stream water TDN concentrations, particularly for catchments with a high prevalence of red alder, with the lowest concentrations occurring in the summer and the highest occurring in November-December. Due to strong seasonality in TDN concentrations and in particular stream flow, over 60% of the TDN export from this watershed occurred during the 3 month period of November-January. Entrainment of marine water into the surface layer of Hood Canal accounted for ≈98% of N loading to the euphotic zone of this estuary, and in a worst case scenario OSS N inputs contribute ≈0.5% of total N loading. Domestic wastewater discharges and red alders appear to be a very important N source for many streams, but a minor nutrient source for the estuary as a whole. [ABSTRACT FROM AUTHOR]