The term "body of groundwater" represents a new administrative tool established by the water framework directive (WFD) in order to manage European groundwaters. Its practical application raises some difficulties due to unclear definitions and the large heterogeneity of European aquifers. In this work, a methodology is proposed to carry out the delineation of bodies of groundwater according to the requirements of the WFD. This methodology faces up to some of the major difficulties that can arise during the delineation, such as the identification of bodies of groundwater in multilayered aquifers, boundaries between superposed groundwater bodies, and delimitation in low permeability materials or in dismembered aquifers. In order to show its practical application, the proposed methodology is applied in a pilot Mediterranean river basin located in southern Spain. Results show that previous knowledge of the hydrogeological conditions is necessary to enable a correct delineation of groundwater bodies. Finally, alternative procedures are proposed for low permeability and small aquifers in order to reduce the number of groundwater bodies identified and simplify their overall management.