The intensive utilization of tropical inland water bodies for multiple and sometimes competing activities underlines the necessity for their integrated and holistic co-management. This paper presents our synthesis on lake and reservoir fisheries in South and Southeast Asia as social–ecological systems, based on a synopsis of our research findings from a previous EU-funded research programme in Sri Lanka, Thailand and the Philippines (FISHSTRAT project). The paper attempts to merge our results with recent developments in research, policy and practice. We explore the effects of the main external and internal control mechanisms of the trophic state and pinpoint to the high production potential of traditionally unexploited small indigenous fish species. The limitations of conventional centralized management systems highlight the importance of introducing transdisciplinary approaches which integrate limnology, fish ecology and fisheries with the interests of other resource using stakeholders and decision makers in order to develop locally appropriate co-management strategies for sustainable aquatic resource use.