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The European Water Framework Directive (WFD) constitutes a new view of water resources management and provides a challenge in the development of new and accurate methodologies for the classification of water bodies. It is necessary to improve and develop approaches based upon scientific knowledge in order to achieve requirements of comparability throughout European waters. This contribution focuses on the development of a classification typology for a series of wetlands in southern Spain, based on hydromorphological elements. Spanish wetlands and playa-lakes are usually small (< 50 ha) and temporary and, for that reason, only indirectly addressed in the WFD with respect to the status of ground water dependent ecosystems. The WFD does not provide any guidance on how to react to significant pressures and impacts on such ecosystems. In order to manage, protect and, if necessary, restore this type of water bodies, it is important to classify them according to the main factors involved in their hydrological functioning. The water balance of the playa-lakes has proved to be a valuable tool to determine the hydrological regime in a semi-arid climate. Surface-groundwater relationships are key elements in determining the water balance, but there are other elements that could indicate or corroborate the hydrological functioning of a playa-lake, such as hydro-chemical markers or morphometric indexes. The present work could constitute the basis for a discussion document for other regions and countries throughout Europe and elsewhere.