The main purpose of this study was to evaluate the effect of alternative cropping systems on farm net returns, and nitrate-N and sediment yields in Thomas Brook Watershed (TBW). The study involved integrated bio-physical and economic optimization modelling. Crop yield and nitrate-N pollution response functions were estimated and then used in trade-off analysis between farm returns and environmental quality improvement. Five crop rotation systems were evaluated for seven fertilizer levels under conventional tillage (CT) and no-till systems (NT). Nitrate-N leached, as well as estimated maximum economic rate of N (MERN) fertilizer level and marginal abatement costs depended on crop type, rotation system, and tillage type. The most cost effective cropping systems that met restrictions on Health Canada maximum limit on nitrate-N in water included corn-corn-corn-alfalfa-alfalfa under NT for corn-based cropping systems, potato-winter wheat-carrot-corn under CT for vegetable horticulture-based and potato-barley-winter wheat-potato-corn under NT for potato-based cropping systems.