Intensive tillage (IT) in potato crops is considered as one of the main non-point sources (NPS) of local water eutrophication in the Fuquene Lake of Colombia. Therefore, the local government has invested in several programs aiming at the adoption of principles of conservation tillage (CT) which would allow for developing and applying the agricultural best management practices (BMPs). The complexity of hydrological and geological heterogeneity makes the degree of benefit that CT has in different locations uncertain. In this study, the Soil and Water Assessment Tool (SWAT) was used to assess the impacts of changing IT for CT on nitrogen (N) and phosphorus (P) losses in surface water runoff from the potato crop in the Fuquene watershed. This is done at field and watershed levels. A two-year study quantified the changes in surface water runoff pollutants for three potato crop cycles under the traditional IT practice and CT practice - which included reducing tillage, green manure, and permanent soil cover - at twelve runoff plots installed in the Fuquene watershed (Quintero and Comerford, 2013). This information was used to build, calibrate and validate the SWAT model. The results suggest that CT for the Fuquene watershed can be reduced up to 26% of the sediment yield and 11% of the surface runoff compared with IT, which means an overall reduction of load. The main CT effect on nutrient losses in runoff is an increase in the total N and P (2% to 18% respectively) compared to IT. However, the results at watershed level showed different patterns from those obtained at field level. Despite the model uncertainties, the results show a possibility of using hydrological models to assess the effectiveness of various field management practices in agriculture.