In the present study, the treatment of dairy industry wastewater using bacterial biomass isolated from eutrophic lake sediments was carried out to produce water for agricultural use. Microorganisms were isolated from lake sediment to establish bacterial consortiums efficient in the removal of organic matter from dairy wastewater. The nature of the effluents varied according to the treatment system and parameter evaluated. In the anaerobic treatment, chlorides, sulfates, phosphates and chemical oxygen demand recorded the highest average values. In the aerobic treatment, turbidity, electrical conductivity, ammonium, total suspended solids and biochemical oxygen demand recorded the highest average values. The analysis of the percentage of similarity of the anaerobic (BSI1) and aerobic (BSI2) bacterial consortia with a contribution of more than 1% revealed a 91.38% contribution. In anaerobic reactors the orders Clostridiales (14.27%) and Lactobacillales (12.44%) predominated and in aerobic reactors the order Burkholderiales (20.67%).