The present investigation was performed in the wastewater treatment batteries of ENACAL-Sutiava, located in the department of León, in the period March-August 2015. The aim was to evaluate the dynamics of the concentrations of the free metabolites (glucose and amino acids) and its relationship with physical and chemical parameters. Once a month, readings of the physical and chemical parameters (temperature, pH, dissolved oxygen and turbidity) were taken. Water samples were taken to evaluate the concentrations of the metabolites. In general, the concentration of the oxygen-pH-turbidity parameters show an increasing behavior in the direction primary-secondary batteries, in the batteries of modules A and B. The concentration of free amino acids in the body of water was always significantly higher than the concentration of glucose in all the batteries of modules A and B. The battery module B showed increasing behavior of the concentration of amino acids in the direction primary-secondary batteries, similar to the behavior observed in the physicochemical parameters oxygen, pH and turbidity.