The modern legislative framework for environmental protection places a strong emphasis on the “ecosystem approach” to the management of freshwater and marine habitats. Implicit in this approach is recognition of the complex interactions between components of the ecosystem, both physical and biological, that result in ecosystem service flows. Hydrodynamic conditions are a first order physical driver for aquatic systems, initially regarded as the physical context that controlled the abundance and distribution of organisms. The corollary of this, that the biota can manipulate, modify, and resist flow is now much better recognised. However, the recognition of a principle and the understanding of the active mechanisms, to the point at which useful predications can be made, is quite different. Observations of the importance of sea grasses, saltmarsh plants and mangroves for the physical biostabilisation of habitats are now being supplemented by work on the microbial world including bacterial biofilms, microbial mats, epiphytic microalgae and living stromatolites. This presentation traces some of the history of the development of biostabilisation as an area of research and includes examples across varied ecological settings and provides a discussion of the current understanding of ecosystem function in terms of the response of biota to flow and consequent effects on ecosystem dynamics.