The effluent from the primary settling tank is taken for secondary treatment, where the primary effluent is passed into large-aeration tanks with constant agitation, and the air is pumped into it. Aeration tanks show vigorous growth of useful aerobic heterotrophic microbes into flocs (mass of bacterial and fungal filaments). The microbes consume a significant part of the organic matter and significantly reduce the BOD of the effluent. The effluent is passed into a secondary settling tank where bacterial flocs are allowed to sediment to form activated sludge.

A part of activated sludge is fed into anaerobic sludge digesters, where the anaerobic methanogenic bacteria digest the organic matter present in sludge to produce biogas, used as sources of energy.