The Gowienica Miedwiańska catchment is a small agricultural catchment located in the NW of Poland draining into Lake Miedwie, on which a drinking water source for the city of Szczecin is located. The catchment is characterized by very rich soils. Subsequently, agriculture is intensive and this is thought to influence the poor water quality in the local area. Despite more than 20 years since first programmes of measures towards protection of water quality have been introduced into the catchment, these have not been produced the expected results, and the local farming community cites other sources such as poor sewage management rather that agricultural activity, as responsible for this problem. Evaluation of flow pathways in the catchment and identification of the areas responsible for the highest impact on local water quality was therefore conducted within the EU funded project Waterprotect. The aim of this study was to clarify sources of pollution precisely in space and time, in order to increase trust from stakeholders, so that targeted measures can be used effectively to improve water quality. The study included water quality monitoring, isotopic analysis and numerical flow modelling. Results showed that water quality in the catchment is spatially and temporally variable. 93% of nitrogen loadings into the Miedwie lake have been attributed to agriculture and only 7% to wastewater inputs. The local hydrology and hydrogeology play an important role in the distribution of the impacts from these inputs. As a result, three sub-catchments were identified which are differentiated by dominant pollution source, land use, and hydraulic characteristics. The highest inputs from agriculture have been identified in the most upper sub-catchment and this area have been pointed out as most suitable for implementation of agricultural best management practices towards protection of water quality at a local level.