The EU Water Framework Directive states that the management of surface water must be based on a site-specific assessment of water quality, that is dependent on land use. As a result, to develop a robust chemical management policy for aquatic ecosystems, the ecotoxicological risk must be strictly related to the local conditions and characteristics of the system. This paper presents a methodology developed to assess the ecotoxicological risk of pesticides to site-specific aquatic ecosystems. Spatial and relational databases, provisional models and risk indices were integrated into Geographical Information Systems (GIS) to produce maps of exposure, effect and risk at watershed scale. Each active ingredient is characterised by a data set that includes input data as well as results represented by a risk assessment cartography. The aim of this procedure is to perform a site-specific risk assessment by integrating geographical distribution of predicted environmental concentrations (PECs), ecotoxicological effects and the potential/actual quality of the exposed ecosystem. Examples of pesticide risk maps for surface waters in Lombardia Region (Northern Italy) are shown.