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We demonstrate a linking of moderately high resolution (1 km) terrestrial hydrological models to a 3‐D ocean circulation model having similar resolution in the northern Gulf of Alaska, where a distributed line source of freshwater runoff exerts strong influence over the shelf's hydrographic structure and flow dynamics. The model interfacing is accomplished via mass flux boundary conditions through the ocean model coastal wall at all land‐ocean adjoining grid cells. Despite the high runoff volume and lack of a coastal mixing estuary, the implementation maintains numerical stability by prescribing depth invariant and surface‐intensified inflows at fast and slow discharge grid cells, respectively. Based on comparisons against in situ hydrographic data, the coastal sidewall mass flux boundary condition results in more realistic hindcast surface salinity and salinity gradient fields than models that distribute coastal runoff in the form of spatially distributed precipitation. Correlations with observed thermal and haline monthly anomalies reveal statistically significant hindcast temporal variability during the freshet season when the signal‐to‐noise ratio is large. Comparisons of ocean models forced by high‐ and low‐resolution hydrological models reveal differences in salinity, surface elevation, and velocity fields, highlighting the value and importance of accurate coastal runoff fields. The model results improve our understanding of the regional influence of runoff on sea level elevations and the distribution and fate of fresh water. Our approach has potential applications to biogeochemical modeling in regions where distributed line source freshwater coastal discharges deliver heat, momentum, and chemical constituents that may influence the marine carbon pump.