The estuarine ecosystem is the integration of the physical system represented by sediment and hydrodynamics and the biological system represented by the flora and fauna living in the physical system and the ongoing biological processes. From the viewpoint of sediment dynamics, the interactions between these systems may be described by integrated biogeomorphological research taking into account the biological influences on sediment behavior and transport. This chapter deals with some of the most important ways in which biology and biological processes affect sediment-transport processes and sedimentary environments.