Physio-chemical processes in lake and estuarine system regulate the water quality of these systems. Understanding the rate of transport of chemicals to and from the sediments and the transformation processes in both the sediment and water column are essential knowledge for maintaining the health of lakes and estuaries. Pulse inputs during floods, concentration during droughts and chronic slow releases on these processes and their impact at the short and long-term on water quality are needed if the water bodies are to be maintained. Modelling provides a means to understand, interpolate and extrapolate information on physio-chemical processes in such water bodies. We invite authors to present papers showing how modelling has been used to enhance the knowledge of physio-chemical process in lakes and estuaries and how it has assisted in the management of such systems.