Numerous different types of waste compositions generally in an aqueous environment are bio-remediated under aerobic conditions utilizing highly diverse and multiple microorganisms within a reactor. The process is carried out with the microorganisms attached or bound by a variety of different surface characteristics to packing substrates, located within the reactor, having high surface areas and high porosity in the form of small micropores. Multiple different types of substrates are utilized that include minerals, carbon compounds, polymers and plastics, ceramics, metals, and the like and shapes thereof are utilized that efficiently dissolve air into the water. The reactors desirably have multiple bio-remediation stages therein. The reactor also contains at least one perforated chimney through which air can flow and optimize dissolving oxygen into the aqueous environment of the various bio-remediation stages. The reactors house maximum biodiversity to bio-remediate waste compositions in various wastewaters encountered from industrial, commercial, municipal and residential sources.