Human activities (e.g. agriculture and industry) have been increasing within the river basins. These agricultural and industrial impacts affect the water quality in the basin and the related ecosystem and ecosystem services. We aim to identify the link between water management options and ecosystem services, and how the ecosystem services change when certain management actions are applied. Thus, a case study in the Guayas River basin (Ecuador) is presented. A trade-off tool was developed to assess ecosystem services. A model was developed with both biophysical and management variables as input to calculate the effect on multiple ecosystem services (food production, fresh water availability and recreational value). With these three ecosystem services, a trade-off tool was constructed with the use of Bayesian Belief Networks (BBNs). Based on the model outcome, it can be stated that in general, the changes in management leading to an increase in food production, made the fresh water availability and recreational value go down. With further research on the influences of different variables on ecosystem functions and services, this BBN model can become a valuable trade-off tool to be implemented in both water and environmental management and decision making.