Nitrate and pesticide contamination of surface and groundwater has become a major problem in intensive farming regions in Europe, with nitrate concentrations reaching values above the standard defined in 2000 by the European Water Framework Directive. In the Seine basin, a major issue is the closure and abandonment of drinking-water wells, which force water managers and drinking-water producers to explore solutions for water resource protection. Organic farming has appeared as a credible alternative to conventional farming, and this study explores the potential of organic farming to reconcile agricultural production and water quality. On the basis of agricultural statistics, survey questionnaires and experimental data, the nitrogen soil surface balance (N-SSB) has been established at the scale of a small 104-km 2 catchment (The Orgeval sub-basin), representative of the intensive cash crop farming in the Seine basin. The N-surplus for arable land in specialized organic cash crop systems has been found to be half that of current conventional systems (15 kg N ha À1 yr À1 versus 30 kg N ha À1 yr À1 , respectively). The N-yield in organic systems is 21% lower than in conventional systems, but total fertilization (mostly symbiotic N fixation) is also 26% lower. Whereas 2–3 years of forage legume (e.g., alfalfa) as a starter crop of the typical 7-to 10-year diversified rotation builds up N soil fertility and helps prevent weeds without pesticides, the existence of an outlet for this fodder production is a limiting factor for the economic sustainability and the environmental benefits of these farming systems. Therefore, we explored the possibility of a reconnection of livestock and crop farming systems in the Orgeval catchment, a traditional dairy farming and Brie cheese production region. We calculated the N-SSB for this type of a reconnected livestock and cropping system and found a value very close to the specialized organic cash crop system with full utilization of fodder production, leading to profitable animal production, essentially as milk in this farm design. This reconnected system is compared with the estimated situation in 1955 before separation of plant and livestock production. Furthermore, the N-SSB values were converted into infiltrating sub-root concentrations and used as a boundary condition to a biogeochemical model. Organic cropping and organic reconnected livestock cropping systems result in a 50% reduction of surface water nitrate concentrations, a surface water quality 20% better than that reconstructed for 1955, with an overall higher protein production.