One of the main challenges of water management in developing countries is to control the impact of the urban environment on the natural environment. Identifying sources of pollution in an urban watershed is a critical first step towards providing more integrated environmental planning, proper wastewater disposal and public water supplying. Thus, in this study we assessed 5-year water quality data from six urban river basins in Southern Brazil. In addition to the principal component analysis (PCA), three indexes were evaluated individually: Water Quality Index (WQI), Toxicity Index (TI) and CCME WQI framework (CCME WQI). In order to evaluate the effect of land use, the monitoring sites were assessed according to the urbanization criteria. The application of PCA revealed the existence of six components, explaining 73.78% of data variation. The component that explains most of the variation in water quality (30.80%) is associated with domestic wastewater. The second component showed a strong dependence (29.44%) on industrial activities such as electroplating and metalworking in determining the water quality, while the other components are related to certain industrial and agricultural activities. Likewise, the application of WQIs demonstrated similar results to the PCA. WQI and TI showed scenarios of concern regarding public supply. CCME WQI presented a significant disparity between the assessed watersheds and the Brazilian legal framework goals. Studies in this field significantly contribute to the establishment of environmental licensing criteria, by demonstrating patterns and environmental features. In addition to it, one can identify which watersheds demand greater attention with respect to control and recovery of proper environmental conditions. Furthermore, it can provide support for revisions in urban and watershed planning, especially in qualitative aspects eluding conflicts over water use in future scenarios.