The present investigation was carried out in Salinas Grandes stuary, department of León, in the period June-November 2017. The aim was to evaluate the fluctuations of the concentrations of the groups, Chlorophytes, Cyanophytes, Diatoms and Dinoflagellates and relate them to the variation of physical-chemical parameters. The water samples were taken once a month, the physical chemical parameters were measured (salinity, oxygen, temperature, pH and turbidity). In general, our results show the presence of the four groups of microalgae, being Diatoms and Chlorophytes the groups that presented higher concentrations. With regard to salinity, the month of July shows the highest concentration (34.66 ppm), decreasing over time in the whole area. Dissolved oxygen ranged between 4.53-0.72 mg / L throughout the study period. The maximum temperature values were presented in the month of August (30.23 ºC), without significant changes in time and between sampling points. With regard to turbidity, readings ranged between 31.66-120 cm, with June being the month with the lowest readings. Throughout the study period, the pH value of the water presented a range of (7-8.83). There is no correlation between the fluctuations of the main physicochemical parameters; therefore, this area of study does not present conditions that guarantee animal welfare for the development of fish culture in floating cages.