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As part of ECOManage, an international project aimed at providing modeling and decision-making tools for coastal zones to governmental authorities and concerned citizens, the SWAT model was applied to the Aysn River Basin of Southern Chile. The overall goal for SWAT use is to predict nutrient loading to the Aysn Fjord under different development scenarios. This paper presents important first steps in the use of SWAT in a basin that spans the Southern Andes and presents an order of magnitude of difference in annual precipitation from east to west. Often viewed as a pristine area by visitors to the area, the basin has experienced major forest fires and severe erosion in the last century. We report on the hydrodynamic calibration of SWAT for the Aysn basin and describe modifications to the SWAT code and landuse database that were needed in order to adequately describe the production of biomass and nutrient cycling. Despite temporal and spatial gaps in the data available for the basin, a Pearson product-moment correlation coefficient of 0.55 and a Nash-Sutcliffe efficiency of 0.45 were obtained for the first calibration phase, indicating an adequate fit between observed and predicted values. We also report on annual loads of nitrogen and phosphorus to the Aysn basin using the OSPAR HARP Guidelines, a first step in the development of TMLDs for the basin. We mention what SWAT application has taught us about this largely unstudied basin. Finally, we mention future steps that include the calculation of TMDLs with the MOHID model, a multi-component hydrodynamic and water quality model used in estuaries around the world.