The Oualidia Lagoon is a semi enclosed marine ecosystem connected to the Atlantic Ocean of Morocco and exposed to human activities, mainly agriculture and oyster farming. The present study aims to characterize the spatio-temporal variation of the phytoplankton assemblage and to highlight the effect of the main environmental parameters on this important planktonic component evolving in a vulnerable anthropized ecosystem. For this purpose, a field survey was carried out during four seasons in 2011 to determine the biotic (phytoplankton, chlorophyll a) and abiotic (temperature, salinity and nutrients) variables during low and high tide periods. Results highlight an established spatial variation of physico-chemical parameters especially at low tide, with contrasted environmental conditions between the upstream and downstream zones. The phytoplankton diversity and abundance were characterized by a pronounced seasonal pattern. The Oualidia Lagoon is a nutrient rich ecosystem, especially in its upstream part. We also showed that both planktonic diversity and abundance were maximum in autumn and summer. The phytoplankton richness is governed by two main factors: the seasonality of nutrient enrichment and the regular supply of Atlantic seawater. Nitrate and ammonium were the main environmental abiotic factors determining the development of phytoplankton populations. The dynamic of phytoplankton in the Oualidia Lagoon is highly influenced by marine waters incoming from the Atlantic Ocean especially during the upwelling season. Finally, potential harmful algal species belonging to different genera such as Pseudo-nitzschia, Alexandrium, Prorocentrum, Dinophysis, Ostreopsis, Karenia, Coolia, Gonyaulax, Gymnodinium, Dictyocha and Chattonella were encountered showing a potential in this ecosystem to develop noxious blooms.