Reactive nitrogen (N) emissions have increased over the last 150 years as a result of greater fossil fuel combustion and food production. The resulting increase in N deposition can alter the function of ecosystems, but characterizing its ecological impacts remains challenging, in part because of uncertainties in model-based estimates of N dry deposition. Here, we leverage the tiled structure of the land component (LM3) of the Geophysical Fluid Dynamics Laboratory (GFDL) Earth System Model to represent the impact of physical, hydrological, and ecological heterogeneities on the surface removal of chemical tracers. We show that this framework can be used to estimate N deposition at more ecologically-relevant scales (e.g., natural vegetation, water bodies) than from the coarse-resolution global chemistry–climate model (GFDL-AM3). Focusing on North America, we show that the faster removal of N over forested ecosystems relative to cropland and pasture implies that coarse resolution estimates of N deposition from global models systematically underestimate N deposition to natural vegetation by 10 to 30 % in the Central and Eastern US. Neglecting the subgrid scale heterogeneity of dry deposition velocities also results in an underestimate (overestimate) of the amount of reduced (oxidized) nitrogen deposited to water bodies. Overall, changes in land cover associated with human activities are found to slow down the removal of N from the atmosphere, causing a reduction in the dry oxidized, dry reduced, and total N deposition over the contiguous US of 8 %, 26 %, and 6 %, respectively. We also find that the reduction in the overall rate of removal of N associated with land-use change tends to increase N deposition on the remaining natural vegetation and facilitate N export to Canada. We show that subgrid scale differences in the surface removal of oxidized and reduced nitrogen imply that near-term (2010–2050) changes in oxidized (−47 %) and reduced (+40 %) US N emissions will cause opposite changes in N deposition to water bodies (increase) and natural vegetation (decrease) in the Eastern US, with potential implications for acidification and ecosystems.