This paper highlights the findings of a desktop study on the status of eutrophication of lakes in Malaysia. It aims to take stock of the current status of the lakes in the country and the threats to ecosystems. This baseline study, together with its recommendations for remedial measures and environmental strategies, form the foundation for better planning, research and management of lakes in Malaysia. The research needs on lakes in Malaysia were also identified by benchmarking with the level of lake research in the US and Japan.