Our work was aimed to study the phytoplankton communities in two coastal sites placed in Natural Reserve "Lake of Tarsia-Mouth of river Crati" in Northern Ionian Sea-Calabria (Italy). This zone represents a wetland area of high natural interest populated by different organisms (animals and plants) living in a transitional ecosystem characterized by a great biodiversity. The sampling was performed in two different seasonal periods (summer and autumn 2012) and in two different sites (marine site vs fluvial one). Different algal genera/species were recognized and analyzed by Utermöhl inverted microscope method and also qualitative and quantitative measures of biomass were performed. The results showed that the dominant group was the Diatoms with exclusive species in such periods in both the sampling sites; we also observed the presence of genera and/or species of potentially toxic algae (Pseudo-nitzschia sp., Alexandrium taylori, Prorocentrum micans, Skeletonema sp.), mostly in summer. Complessively, the phytoplankton biomass was always higher in marine site than in the fluvial site. The results were also processed considering the context of the chemical-physical parameters (such as temperature, pH, salinity, nutrients). The high concentration of the nutrients N and P in such periods indicated a state of meso-eutrophic waters both in the proximity of river site as well as in the marine zone. The data represent the first contribution to the knowledge of the phytoplankton structure in this area, which results in a very variable environment with a high recovery capacity.