The Ria Formosa natural park, located at the south coast of Portugal, harbours an exceptional landscape and a repository for microbial scientists. The natural park is meandered by the Ria Formosa lagoon (upper picture), a multi-inlet mesotidal system, that feeds to an adjacent solar saltern (lower pictures). The lagoon allows unrestricted distribution of protistan plankton along a salt gradient ranging from brackish (around 30 psu) to hypersaline conditions (up to 360 psu). This natural system provides an excellent opportunity to study structural and functional responses of protistan plankton to salinity gradients. Structural aspects are i) the identification of environmental barriers, ii) the assessment of environment-specific diversification in protistan plankton, iii) the evaluation of protistan distribution patterns and rules, compared to bacteria, archaea and macroorganisms along chemical gradients and iv) the integration of the obtained data into models predicting changes in plankton composition in the light of global climate changes. As the ability of protists to react to and cope with gradients in osmotic pressure and ion concentrations has barely been studied, another major aspect is the revelation of metabolic responses to salinity in general and salinity shifts in special, like local adaptations.