Rainfall runoff and leaching are the main driving forces that nitrogen, an important non-point source (NPS) pollutant, enters streams, lakes and groundwater. Hydrological processes thus play a pivotal role in NPS pollutant transport. However, existing environmental models often use oversimplified hydrological components and do not properly account for overland flow process. To better track the pollutant transport at a watershed scale, a new model is presented by integrating nitrogen-related processes into a comprehensive hydrological model, the Distributed Hydrology Soil and Vegetation Model (DHSVM). This new model, called DHSVM-N, features a nitrate transport process at a fine resolution, incorporates landscape connectivity, and enables proper investigations of the interactions between hydrological and biogeochemical processes. Results from the new model are compared with those based on Soil & Water Assessment Tool (SWAT). The new model is shown capable of capturing the “hot spots” and spatial distribution patterns of denitrification, reflecting the important role in which heterogeneity of the watershed characteristics plays. In addition, a set of control experiments are designed using DHSVM-N and its variant to study the respective role of hydrology and nitrate transport process in modeling the denitrification process. Our results highlight the importance of adequately representing hydrological processes in modeling denitrification. Results also manifest the importance of having a good transport model with accurate flow pathways that considers realistic landscape connectivity and topology in identifying the denitrification hot spots and in properly estimating the amount of nitrate removed by denitrification.