A controlled eutrophication system and process are disclosed. The system includes the combination of a partitioned aquaculture system in conjunction with an anaerobic digester. Wastewater containing pollutants, such as nitrogen and phosphorus, are fed to the partitioned aquaculture system. Algae within the system converts the pollutants into algal biomass. Fish populations, in turn, control the algal populations. The fish populations may then be periodically harvested for human or animal consumption. A polishing chamber is contained in the system in which aquatic organisms remove substantial amounts of the algae from batch fed additions of water. The water is then discharged to an external water source containing virtually no pollutants. In one embodiment, the biomass excreted by the aquatic organisms in the system are collected and fed to a digester. In the digester, the biomass is converted to a hydrocarbon gas and collected for its fuel value, while the liquid fraction is collected for its fertilizer value.