A method and apparatus for building a lagoon based advanced treatment system or upgrading an existing lagoon system for advanced treatment of wastewater. The lagoon is provided with a baffle to create a complete mix zone in which an aeration system and bioconcentration modules are installed. Biological solids are concentrated in the modules and drop through their open bottoms where the solids are recirculated and mixed by the aeration system. Once a biomass equilibrium is reached in the complete mix zone, excess solids are passed into the rest of the lagoon for standard treatment there. The complete mix zone is operated as a low rate activated sludge process with a detention time much less than for the rest of the lagoon, maintaining sufficient heat and sludge aging to effect complete biological nitrification and/or denitrification.