Atmospheric deposition accounts for up to a third of the nitrogen input into the Baltic Sea and contributes to eutrophication. It is useful to use three-dimensional biogeochemical models to evaluate the contribution of atmospheric nitrogen deposition to eutrophication because bioavailable nitrogen impacts eutrophication differently depending on time and place of input – e.g. nitrogen is processed and denitrified faster in flat coastal regions. The western Baltic Sea, which is stressed by high nutrient loads, is characterized by many small islands and a wrinkled coast line. In regions with this type of coastal features, the grid resolution of atmospheric chemistry transport models (CTMs) has a strong impact on the modeled nitrogen deposition. The aim of this study was to evaluate the benefit of finer spatially resolved deposition data as input for simulations with the ecosystem model ERGOM. This study also focused on the shipping contribution to the marine nitrogen budget via deposition of shipping-emitted nitrogen oxide (NO_x). Differences in the modeled dissolved inorganic nitrogen (DIN) caused by refined nitrogen deposition were identified in some coastal sections and between the Danish islands. Patches of enhanced DIN concentrations were found distant to the coast in model runs forced by the finer resolved data. These were caused by better resolved precipitation events. The differences between fine and coarse resolution deposition of the same CTM were low compared to the difference to EMEP deposition, which was a third comparison data set. The shipping sector contributed a maximum of 10 % and on average less than 5 % to DIN. In summary, particularly small scale ecosystem model studies in bights are expected to benefit from spatially higher resolved nitrogen deposition data. The shipping sector is a relevant contributor to the marine nitrogen deposition but its contribution to the marine DIN pool is rather low.