Bio-economic models can be used to assess the impact of policy and environmental measures through economic and environmental indicators. Focusing on agricultural systems, farmers’ decisions in terms of cropping systems and the associated crop management at field scale are essential in such studies. The objective of this paper is to present a study using a bio-economic model to assess the impact of the Nitrate Directive in the Midi-Pyrenees region (France) by analyzing, at the farm scale, farm income and three environmental indicators: nitrate leaching, erosion and water consumption. Two scenarios, the 2003 CAP reform (baseline scenario) and the Nitrate Directive (policy scenario), with a 2013 time horizon, were developed and compared for three representative arable farm types in the Midi-Pyrenees region. Different types of data characterizing the biophysical context in the region (soil, climate), the current cropping systems (rotation, crop management) and farm resources (irrigated land, labor) were collected to calibrate and run the models. Results showed that the implementation of the Nitrate Directive may not affect farm income. However, significant modifications to cropping systems and crop allocation to soil types were simulated. Contrary to expectations, nitrogen leaching at the farm scale did not change. Overall water consumption increased and soil erosion decreased due mainly to a modification in cropping patterns and management by soil type. This study provides an example of unanticipated effects of policy and trade-offs between environmental issues.