One of the major challenges in environmental life cycle assessment (LCA) of crop production is the nonlinearity between nitrogen (N) fertilizer inputs and onsite N emissions resulting from complex biogeochemical processes. A few studies have addressed this nonlinearity by combining process-based N simulation models with LCA, but none accounted for nitrate (NO3-) flows across fields. In this study, we present a new method, TNT2-LCA, that couples the topography-based simulation of nitrogen transfer and transformation (TNT2) model with LCA, and compare the new method with a current LCA method based on a French life cycle inventory database. Application of the two methods to a case study of crop production in a catchment in France showed that, compared to the current method, TNT2-LCA allows delineation of more appropriate temporal limits when developing data for on-site N emissions associated with specific crops in this catchment. It also improves estimates of NO3- emissions by better consideration of agricultural practices, soil-climatic conditions, and spatial interactions of NO3- flows across fields, and by providing predicted crop yield. The new method presented in this study provides improved LCA of crop production at the catchment scale.