The present study was made in the Salinas Grandes estuary, located in the community of Salinas Grandes, department of León, in the period of June-November 2017. The aim was to evaluate the dynamics of the concentrations of the microalgae groups, Chlorophytes, Cyanophytes, Diatoms and Dinoflagellates and relate them to the fluctuation of the physicochemical parameters. The water samples were taken once a month, using 500 ml bottles and the physicochemical parameters were measured (temperature, salinity, dissolved oxygen, turbidity, pH). The results show, in a general way, the presence of only three of the four main groups (Chlorophytes, Diatoms and Dinoflagellates). Diatoms showed higher concentrations and diversity of genera, showing significant difference (P≤0.05) with the other two groups, which is logical considering the proximity of the sampling area with the sea. Also, a decreasing tendency in the concentrations of these is shown as it advances towards the continent. Diatoms and dinoflagellates showed positive correlation in the three study areas. Likewise, a positive correlation was observed between the levels of dissolved oxygen and turbidity, which suggests that the phytoplankton fluctuation is the one that modulates the concentration of dissolved oxygen.