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 was carried out. The results indicate a significant increase in phytoplankton density between 2500 and 67,300 cells/mL compared to previous data of 1981 (between 10 and 500 cells/mL). Concentration of Chlorophyll-a arrives to 13 mu g/L and transparency of water reduces to 1.3 m according to Secchi disk depth. The presence of Chlorophyceae, Chrysophyceae, and nanoplanktonic Cryptophyceae stands out, while species diversity drops significantly. Observing the evolution of the lagoon, we can deduce that eutrophication process could increase. To avoid this, it would be necessary to implement control measures for the use of fertilizers in nearby growing areas and to study water treatment techniques to reduce nitrogen inputs so that phytoplankton densities can decrease.