Environmental gradients caused by hydrological changes, whether natural or maninduced, affect the planktonic taxonomic and functional composition in shallow water ecosystems. In this sense, our aim was to find out the main variables or variable ratios that are the driving forces of the major phytoplankton taxonomic groups in Mediterranean coastal lagoons. For this purpose, 11 waterbodies were choosen, 6 of them in Empordà wetlands and 5 in the Doñana National Park, looking for representative conditions along a gradient of salinity and nutrient content. Two surveys were conducted in each waterbody (January and May 2007), after that the phytoplankton composition (chemotaxonomic composition) and also several physical and chemical environmental variables were analyzed. Two methodological approaches were used and compared: a first approach with a log (x+1) variable transformation and a second one where variables were transformed using the compositional data analysis (CoDa) techniques introduced by Aitchison (1986). When the raw data approach and the CoDa approach analysis (RDA) were compared, the results obtained were similar with regard to explained variance and also interpretation. The CoDa approach was characterized by the introduction of a new environmental driving factor, the bacterial biomass, whose ratio with the peptidase enzyme activity became significant. In this sense, the CoDa approach contributed to improving the biological interpretation of the phytoplankton distribution based on the raw analysis