The implementation of National Water Resources Policy instruments depends on detailed information in space and time, on a large scale, within the river basin. This research aims to evaluate scenarios to support water quality management in watershed by modelling with spatio-temporal discretization distributed in a small spatial dimension. The SWAT hydrological model was applied in the Itajai river basin. This hydrographic basin with 15,000 km2 was discretized in 2,103 hydrological response units (HRUs). The model input data for each HRU were fed in, from the quantitative and qualitative aspects. The time series of water quality was obtained in non-systematic monitoring from different sources, such as water supply companies and potential polluting companies, among others. The model calibration and validation were performed, presenting adequate results for both the quantitative and qualitative processes. The scenarios corresponding to current and evolutionary situations of pollutant contribution for four water quality parameters (biochemical oxygen demand, total phosphorus, total nitrogen and thermotolerant coliforms) were analysed. The results are expressed as the mean, median, non-exponential frequency of 80% and reference flow, discussing the statistical index that best represents the pollutant concentrations in the bodies of water. The simulations show that the measures proposed for the water quality management of the basin promote a significant reduction in pollutant concentrations in comparison to the critical scenario. According to the results, it can be affirmed that the discretization of the basin in small contribution areas generates greater results precision of the model. The daily and distributed data in the basin provide localized information, according to the basin ortho coding, supporting the decision in order to support the management of water resources, contributing to the implementation process of the framework of surface water courses in the basin, as well as serving as a generic model for other purposes.