Ó bidos Lagoon is classified as a sensible system according to the eutrophication criteria in the Portuguese Decree-Law 149/2004, which transpose the standards of Urban Waste Water Treatment Directive (Council Directive 91/271/EEC) concerning urban waste water treatment. From September 2005 onwards, the urban loads of five Waste Water Treatment Plant (WWTP) were deviated to a submarine outfall to prevent water degradation and improve the lagoon trophic state (LTS). This paper evaluated the LTS after urban loads diversion, testing the hypothesis behind the management decision. First, the loads reaching the lagoon were determined with the Harp-Nut guidelines and watershed modeling. Then, the water quality in the lagoon was simulated with a hydro-ecological model and compared with measured data. Finally, management scenarios corresponding to nutrient loads reduction were tested to determine hypothesis-driven LTS. Results showed that the loads from pig farms should be diverted instead of the WWTP, to improve the LTS and achieve a ''Good/Bad'' status. The proposed method stresses the importance of integrated modeling tools in the Water Framework Directive, given their skill in testing various hypothesis, and ultimately ruling out inadequate management decisions before implementation.