1 - Data on phytoplankton groups of three lagoons of the Albanian coast (Patoku, Karavasta and Narta) have been reported in this paper. 2 - The phytoplankton growth was relatively low in Patoku and Karavasta. Intense growth was observed in Narta lagoon, with blooming state in April. Bacillariophyceae, Dinophyceae and Cryptophyceae represented the most abundant part of the phytoplankton of these three lagoons. Filamentous Cyanophyceae were present only occasionally, especially in Narta. 3 - About 18 species present in phytoplankton were potentially toxic, but not relevant in lagoons; nevertheless, Prorocentrum minimum was found relatively abundant in spring 2006, in Narta. 4 - Continuous assessment of microscopic algae would inform better about the knowledge of Albanian coastal wetlands; moreover, it would help on the fulfillment of required standards derived from the application of the EU Water Framework Directive (WFD).