Discussion and conclusions are presented from a workshop held at Balatonfured, Hungary in May 2002 on the role of water-level fluctuations on the structure and function of shallow lakes. Water-level regime is regarded to be an important factor for lake ecosystem functioning and affects conservation values. Biota, in particular those living in vegetated areas, respond differentially to changes in hydroperiod dynamics. Extreme water levels may cause shifts between the turbid and the clear, macrophyte-dominated state. Strong effects of anthropogenic changes in the fluctuation of water levels are shown for Mediterranean (Greece, Turkey) and north temperate (The Netherlands) regions. Additionally, effects of climate change are anticipated that might alter the functioning of shallow lakes in these regions differentially. There is a need for data on the relationships between water-level changes and ecosystem responses. A plea is made for international cooperation and information exchange and an internet site for facilitating this has been developed.