Detailed seasonal analyses of phytoplankton assemblages’ composition were performed on long-term datasets (20 years) of two oligotrophic Mediterranean lagoons (Diana and Urbino), in order to test if phytoplankton community and bloom events patterns rely on a seasonal basis. Our results highlight a similar phytoplankton composition between the lagoons, but different patterns in terms of phytoplankton abundances, of timing, magnitude and occurrence of Taxonomic Units, and of bloom events occurrence. Dominant diatoms group showed a seasonal repartition, with highest contribution of Skeletonema sp. during winter and spring, some other groups emerging in warmer seasons (e.g. Chaetoceros spp.), or not showing marked seasonality (e.g. Pseudo-nitzschia spp.). Dinoflagellates’ abundances were higher during autumn, besides exhibiting punctual proliferations over the year. Salinity was the strongest environmental parameter in controlling Diana lagoon phytoplankton community, while Urbino community was mostly controlled by turbidity. A worrying evolution of the toxic diatom Pseudo-nitzschia spp., linked to salinity and temperature changes, was detected in both lagoons. We further demonstrated changes in the phytoplankton community are ongoing in these lagoons, despite their contrasting human pressure contexts, indicating that serious impacts on phytoplankton dynamics and blooms triggering in Mediterranean lagoons shall be foreseen within the current and forecasted climate change scenarios.