Integrated multitrophic polycultures represent an ecologically more sustainable form of aquaculture than monocultures; their economic feasibility relies on proper incentivization by policy makers. Polyculture, combined with a shift to culturing omnivores and herbivores instead of carnivores, reduces the unsustainable use of fish meal and fish oil by commercial aquaculture. The ecological value of any polyculture is proportional to the diversity of feeding niches occupied by the cultured species. The most ecologically sustainable form of polyculture combines all primary trophic levels (primary producers, consumers, decomposers) at appropriate ratios in a fully closed system. Decomposers represent critical links for polyculture systems. They fulfil an essential role in nutrient cycles and are cultured in biofilters and artificial reefs as ATS, periphyton, and bioflocs. Research on biochemical capacities of bacterial decomposer communities affords new opportunities for wastewater treatment. Polyculture systems can be coupled or decoupled, and although coupled systems have some advantages, decoupled systems appear more promising for future development of sustainable aquaculture. Aquaculture integration is not limited to polycultures of aquatic organisms but should also be pursued to link aquaculture and alternative uses of water, including drinking, sanitarian, recreational, conservation, industrial, and agricultural uses. Integration of aquaculture and agriculture (IAA) is practised in two forms: 1) wastewater produced by aquaculture is utilized for irrigation of crops and orchards; 2) animal manure produced by agriculture is used to fertilize semi-intensive aquaculture ponds.