We propose a conceptual model for an Arctic sea that is driven by river runoff, atmospheric fluxes, sea ice melt/growth, and winds. The model domain is divided into two areas, the interior and boundary regions, that are coupled through Ekman and eddy fluxes of buoyancy. The model is applied to Hudson and James Bays (HJB, a large inland basin in northeastern Canada) for the period 1979–2007. Several yearlong records from instruments moored within HJB show that the model results are consistent with the real system. The model notably reproduces the seasonal migration of the halocline, the baroclinic boundary current, spatial variability of freshwater content, and the fall maximum in freshwater export. The simulations clarify the important differences in the freshwater balance of the western and eastern sides of HJB. The significant role played by the boundary current in the freshwater budget of the system, and its sensitivity to the wind-forcing, are also highlighted by the simulations and new data analyses. We conclude that the model proposed is useful for the interpretation of observed data from Arctic seas and model outputs from more complex coupled/climate models.