The bonds between pollution sources, contaminant concentrations and ecological damage are quite complex to access, but the proper management of river basins requires the full understanding of those interactions. In the present study, four SEM-PLS models were used to set up environmental cause-effect relationships in a heavily polluted urban catchment: the Ave River Basin. Data were collected within this watershed relative to point source discharges, diffuse emissions, diffuse indicators (e.g. land use), contaminant concentrations and a Portuguese index of macroinvertebrates diversity (IPtIN). The same dataset was used in the four SEM-PLS models, but each run was based on a different combination of latent variables. In all cases, it was possible to recognize that nitrogen discharges from livestock production, industrial and urban treatment plants are the dominant threats to water quality. The model results were robust, characterized by high, adjusted R Squared values-from 0.744 to 0.931. The models were also used to draw water quality maps. Now, the purpose was to test their prediction capability. Since more than 80% of the water courses were correctly classified for IPtIN, the predictions were considered feasible.