This paper presents a conceptual model of the Zagreb aquifer system. The conceptual model can be applied to groundwater status risk assessment and pollution risk assessment at the local scale, thus satisfying both environmental and preventative/limitation objectives of the Water Framework Directive (WFD) and Groundwater Directive (GWD). Its main purpose is to apply a risk assessment procedure, according to the WFD requirements, and to serve as a foundation for setting up a numerical model of flow in both the saturated and unsaturated zones in order to identify pressure and impact effects on groundwater quality. The model is divided into two parts, taking into account the WFD requirement to assess a risk for a wide range of source-pathway-receptor relationships. The Global Conceptual Model (GCM) provides insight into the processes and pressures at the level of the groundwater system. It contains the geological and hydrogeological characterization of the Zagreb aquifer system and the description of the most significant point and diffuse sources and pathways of pollution and processes influencing pollutant behaviour in saturated and unsaturated zone of the groundwater system. The main pollutants of the Zagreb aquifer system are potentially toxic metals, nitrates, pesticides, pharmaceuticals and chlorinated aliphatics. A Local Conceptual Model (LCM) supports parameterization of the whole groundwater system through the description of heterogeneities and flow and solute parameters of the system components at two sites representing local conditions in the saturated (Stara Loza) and unsaturated (Kosnica) zones. This concept can be regarded as an effective tool for groundwater management of the groundwater system and its compartments and for communicating the conditions in complex groundwater systems with experts, policy makers and general public in an understandable way.<br />