Gipuzkoa (Basque Country, North Spain) is an industrial region where investments in sanitation and wastewater treatment have improved water quality and partially recovered river biological communities. However, further technological improvements are unlikely. Our objective was to assess whether in-stream self-purification may contribute to improvement of the trophic state of rivers. We propose an integrative approach to assessing river water quality, which diagnoses problems, identifies likely causes and prescribes solutions. We first analysed the loads of nutrients transported by Gipuzkoa rivers and compared them with the potential nutrient uptake rates (estimated from published empirical regressions). In reaches where both of them were within one order of magnitude, we considered that the self-purification capacity of river channels may influence nutrient concentrations. Then, we selected some river reaches where no other water quality problems beyond nutrient concentrations occurred and ran the expert system STREAMES 1.0 to diagnose the problems and detect their causes. The studied reaches differed in their problems and in their potential solutions. We empirically determined nutrient retention in two streams by means of mass balances and slug nutrient additions. We detected large differences in retention capacity between reaches and siltation as one of the main problems affecting the self-purification capacity of the study streams. Finally, we used STREAMES 1.0 to identify potential solutions to specific river sections. The results obtained so far point towards an important potential of in-stream bioreactive capacity to reduce nutrient loads and to specific restoration activities that may improve the functionality and trophic status of the streams in Gipuzkoa.