The present paper examines and evaluates the results of a survey carried out to define the criteria for restoring the surface water of the karstic stream “Gravina” (Southern-Italy). The stream runs through a watershed including several agricultural areas. The stream shows an environmental heterogeneity which is of great value to the conservation of biodiversity. The analysis supports a more general water pollution control strategy aimed at safeguarding natural water quality in the urbanized watershed with the aim, also, to reuse partially the water in agriculture. The methodology was based on the surface water sampling, quality parameter analysis and simulation by modelling. The variation and compatibility of wastewater discharge and water stream quality were verified by using a model available in literature in function of biodegradable pollutant load and dissolved oxygen. Several scenarios based on the fixed yield of treatment plants were examined.