Although rivers are the primary source of dissolved inorganic nitrogen (DIN) inputs to the Chesapeake Bay, direct atmospheric DIN deposition and DIN fluxes from the continental shelf can also significantly impact Chesapeake Bay hypoxia. The relative role of these additional sources of DIN has not previously been thoroughly quantified. In this study, the three-dimensional Estuarine-Carbon-Biogeochemistry model embedded in the Regional Ocean Modeling System (ChesROMS-ECB) is used to examine the relative impact of these three DIN sources. Model simulations highlight that DIN inputs from the atmosphere have roughly the same impact on hypoxia as the same gram for gram change in riverine DIN loading. DIN inputs from the shelf have a similar overall impact on hypoxia as those from the atmosphere (~0.2 mg L-1), however the mechanisms driving these impacts are different. While atmospheric DIN impacts dissolved oxygen (DO) primarily via the decomposition of autochthonous organic matter, coastal DIN also impacts DO via the decomposition of allochthonous organic matter entering the Bay from the continental shelf. The impacts of coastal and atmospheric DIN on estuarine hypoxia are greatest in the summer, and occur farther downstream (lower mesohaline) in wet years than in dry years (upper mesohaline). Integrated analyses of the relative contributions of all three DIN sources on summer bottom DO concentrations indicate that impacts of atmospheric deposition are largest in shallow near-shore regions, riverine DIN has dominant impacts in the largest tributaries and the oligohaline Bay, while coastal DIN fluxes are most influential in the polyhaline region. During the winter when estuarine circulation is strong and shelf DIN concentrations are relatively high, coastal DIN impacts bottom DO throughout the Bay.