The response of natural phytoplankton communities, originating from oligohaline brackish water systems, to salinity changes (3–12 PSU) has been studied in small-scale mesocosms. Simultaneously, their reaction on iron manipulations was tested. The experiments, each lasting 7 days, were repeated three times at different dates. Treatments were evaluated with respect to biomass development (Chl a concentration), photosynthesis behaviour, and rough taxonomic composition. The investigated phytoplankton communities were dominated by cyanobacteria. Salt addition was not effective for overall phytoplankton biomass development. Filamentous cyanobacteria, however, were promoted by NaCl enrichments. Dark yield and non-photochemical quenching of fluorescence (NPQ) analyses revealed differences for treatments in dependence on iron supplements. Iron partially seemed to dampen the effects of salt shocks, and iron addition reduced both, capacity and irradiance dependency of NPQ, irrespective of the NaCl treatment.