After the impoundment of the Three Gorges Reservoir (TGR), sediment deposition and related environment problems in the reservoir are issues attracting more and more attention. High nutrients and weak hydrodynamic conditions provide favorable circumstances for the reproduction and growth of the microbes, most of which prefer to adhere to the sediment particles along bed. Biofilm, which are the aggregates of microbes and its extracellular polymeric substances (EPS), significantly changes the sediment properties, including not only the particles themselves but also the transport dynamics. A series of investigations have been carried out through laboratory experiments by our research group. The biofilm was cultivated in the flume with rich nutrients. Under certain hydrodynamic conditions, the bedform induced by the flow and its resistance, as well as the effects of biofilm on the turbulent structure of the flow have been explored for a better understanding of the suspension and transport of the biofilm-coated sediment. Then changes of the settling velocity and incipient velocity were addressed after the biofilm growth. Moreover, a series of experiments for pure and biofilm-coated sediment transport have been conducted in a flume, in which the sediment concentration along the vertical direction and bedload transport were proposed. These studies will contribute to a better management of the water and sediment resources in the reservoir, and give insight to evaluate the ecological effects in and downstream the reservoir.