The Mar Menor is a Spanish coastal lagoon of great ecological and economic interest. The agricultural and tourist activities developed in the surroundings of the lagoon, together with the modifications in its channels of connection with the Mediterranean Sea, have notably affected the quality of its waters, which is altering the natural balance of the ecosystem. In this work, an analysis of the density of phytoplankton present in the lagoon between the months of May to December 2017 has been carried out. There, it has been a notable increase in the density of organisms in post-summer samplings, following the recording of higher temperatures, and the presence of Chlorophyceae, Cyanophyceae, Chrysophyceae and nanoplanktonic Cryptophyceae stands out. The data collected indicate a significant increase in the eutrophication process of the lagoon that requires the development of management plans to reduce agricultural discharges and promote the recovery of the lagoon and its native species.