The present investigation was carried out in the wastewater treatment plant of ENACAL, in the site known as San Isidro stabilization reservoirs, located in the department of León, in the period March-August 2015. The aim was to evaluate the dynamics of the concentrations of the chlorophytes and cyanophytes microalgae groups and relate them to the fluctuation of the physicochemical parameters. The water samples were taken once a month, using 350 ml amber colored bottles and the physicochemical parameters were measured (temperature, pH, dissolved oxygen and turbidity). The results show that, in general, the cyanophytes group are the microalgae that prevailed throughout the study period and differ significantly (P≤0.05) from the chlorophytes group. We identified 15 genera in total, of which 7 genera belong to the chlorophytes group and 8 to the cyanophytes group. Likewise, there is a marked tendency to increase the levels of dissolved oxygen, pH and turbidity as the primary battery-secondary battery-tertiary battery, observing significant differences (P≤0.05) in most months of the study. The batteries module B had a higher number of significant correlations P <0.05 than the batteries module A.