The deterioration of water quality in lakes resulting from unsustainable catchment practices requires concerted efforts to address them, in the form of cooperation among government agencies and institutions, private bodies and the community‐at‐large. Research that provides an understanding of a lake's ecosystem is an important aspect of making informed decisions for sustainable management and governance of lakes. The present study describes the findings of literature reviews on Malaysian lakes, and the national efforts made to establish an agenda for lake research and development in Malaysia directed towards integrated lake basin management (ILBM). The main findings and outcomes of the National Lake Research Blueprint workshop in April 2014 on the issues facing lakes and reservoirs are highlighted. Seven research themes were identified, namely (i) ecosystem services and socio‐economic development, (ii) governance, (iii) water quality and pollution, (iv) eco‐hydrology and basin management, (v) biodiversity and natural products, (vi) physical limnology and hydrodynamics and (vii) technology. The goal is to enhance research and development on sustainable lake basin management directed to conservation and development targets. The findings of this study provide an integrated research framework that can support ILBM governance elements (pillars) elsewhere, and to call for researchers to participate in much‐needed research areas.