Abstract: The present invention is drawn to a unique apparatus and method for treating anaerobic bodies of water including, but not limited to, agricultural waste treatment lagoons. The apparatus and treatment method of the present invention will consist of several phases once the parameters of the wastewater have been ascertained. First, specially selected bacteria are cultivated based upon the wastewater parameters. This specialized bacteria is then utilized in bio-augmentation of the wastewater lagoon. Specifically, bacteria will be isolated and propagated specific for the wastewater which will create a selective dominance within the lagoon and enhance digestion of the waste. The wastewater lagoon is equipped with an aeration means and mixing means such that the wastewater undergoes aerobic digestion utilizing the specially selected bacteria. The solids separation or clarification phase preferably occurs in the existing animal wastewater treatment lagoon.