Theoretical and functional ecology is a source of useful knowledge for ecological engineering. The better understanding of the natural service of water quality regulation is now inspiring for optimization of water resource management, restoration and bioremediation practices. This transfer with a biomimicry approach applies particularly well in the urban, rural and agricultural areas, but is yet underexplored for water quality purposes. This natural service intensely involves the benthic boundary layer as a biogeochemical hot spot with living communities. A selection of processes related to the bioturbation phenomena is explored because of their influence on properties of the aquatic environment. The applications are valuable in a range of fields, from water treatment technology to management of ecosystems such as constructed and natural wetlands, streams, rivers, lagoons and coastal ecosystems. This paper gathers the more obvious cases of potential applications of bioturbation research findings on the biomimicry of natural services to water practices. These include pollution pumping by bioturbated sediment, water column oxygen saving during early diagenesis of deposits under conveyors transport and conservation of macroporous as well as fine sediment. Some applications for constructed devices are also emerging, including infiltration optimization and sewage reduction based on cross-biological community involvement.