Hydroelectric development and regulation have modified the temporal and spatial distribution of runoff entering the Hudson Bay Complex (HBC). To understand the impacts and future of regulation in this region, the numerical ocean model, NEMO, run with the Arctic and Northern Hemispheric Atlantic (ANHA) configuration, is used to model present day freshwater dynamics associated with river runoff and sea ice melt. The present work establishes the freshwater budget in each subregion of the HBC, in addition to evaluating the sensitivity to model resolution and estimates of river discharge forcing. It is shown that the annually averaged HBC freshwater budget is mainly a balance between river discharge and freshwater advected out of the region, while surface fluxes (ice melt and growth, and precipitation and evaporation) are the dominant term on seasonal time scales. Runoff forcing is found to impact the long term mean volume and freshwater fluxes out of the HBC, while increased resolution has minimal effect on these fluxes, with the exception of the Southampton–Baffin Island gate. Quantitative estimates of turbulent, mean, and Ekman components of freshwater exchange between the interior and boundary regions of Hudson Bay are also presented. We use offline Lagrangian passive tracers to estimate the HBC runoff residence time, which is as long as 32 years.