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Addressing the underlying common processes within aquatic systems located in the same geographical region has long been used as a tool for the advancement of limnology. A limnological study of the Merja Sidi Boughaba in 2009 has shown that there are many common features between the physico-chemical and biological conditions of this site and previous data reported from some of the wetlands of the Doñana National Park (South-West Spain). Both are Ramsar sites located on extensive dune systems of the Atlantic coast with a Mediterranean climate. They have a common palaeoenvironmental history that is largely responsible for their similar hydrology and water composition. Oceanic influence has probably produced a slight disproportion of Mg2+ over Ca2+ through airborne sea salt deposition and the surface evaporation of groundwater feeding these wetlands during annual flood and drought cycles. The wide spectrum of environmental conditions encountered in the Doñana wetlands is epitomised by the Merja Sidi Boughaba, where water and sediment gradually change in the same water body from north to south: from humic-coloured waters and a sandy substrate to a calcium-rich substrate with turbid and silted waters which eventually dry out. As a consequence, the community of submersed macrophytes is very rich and dominated by dense charophyte beds. The high primary production coupled with high biodiversity found in the Merja Sidi Boughaba is also shared by the Doñana wetlands. The high conservation status of both sites enables a useful comparison to be made of the water quality of shallow aquatic systems at a regional scale which, contrary to the trophic classifications developed for deep stratified lakes in temperate regions, is not based on regressions between the concentrations of chlorophyll and total phosphorus (Tot-P) but on the proportions of dissolved and particulate P pools. In these Mediterranean sites, nutrients are more efficiently recycled through the sediment (whether deposited at the bottom or suspended in the water column) while seasonal fluctuations of the water level are stronger than in deep stratified lakes and, hence, no significant correlation was found between chlorophyll and either total or particulate P in our study.