In this study we examine how the projected climate change driven decrease in the Baltic Sea salinity can impact the growth, cell size and shape of the recently invaded dinoflagellate Prorocentrum cordatum. In laboratory treatments we mimicked salinity conditions at the edge of the mesohaline south-eastern Baltic and oligohaline-to-limnic Curonian Lagoon. We used an innovative computer-based method allowing detection of P. cordatum cells and quantitative characterization of cell contours in phytoplankton images. This method also made available robust indicators of the morphometric changes, which are not accessible for an expert studying cells under light microscope. We found that the salinity tolerance limit of P. cordatum ranges between 1.8 and 3.6, and that the mean cell size of its population is inversely proportional to both salinity and nutrient content. Under ambient south-eastern Baltic salinity (7.2) the nutrients were stimulating the growth of P. cordatum; while at the edge of its salinity tolerance the nutrient availability did not have such effect. We suggest that in the future Baltic the decline insalinity and increase in nutrient loads may result in larger cells of P. cordatum and extended duration of their presence in plankton, causing longer periods of algal blooms.