The sparse body of information on the ecology and biodiversity of one of the world’sancient lakes, Lake Lanao, was reviewed to arrive at objective insights that may be useful for an ecosystem-based management of the Lake Lanao Watershed. The terrestrial portion of the watershed is relatively rich in flora and fauna that mostly inhabit the remaining intact forests which provides 60% cover, but a thorough species inventory is wanting. Nearly 90% of the alienable and disposable lands including most of the lake shoreline and the adjacent lowland forest areas have now yielded to agriculture (87%), but only 0.4% to urban and rural settlements. Major rivers and numerous intermittent tributaries that sustain lake water are unstudied. Within a span of 30 years since a rich indigenous community of fish species was first described, the lake’s fisheries ecosystem has undergone a regime shift featuring the dominance of invasive fish species and the catastrophic disappearance of 16 endemic cyprinid species. Analysis of nutrient levels when the lake was at its relatively pristine state indicated a high sensitivity to levels of dissolved nitrogen with a pelagic ecosystem that is bottom-up or resource controlled. Most recent water quality analyses indicate a eutrophic, coliform-contaminated, and invasive species-colonized state with anthropogenic input as the possible main driver. Hence, apart from biodiversity conservation in the lake watershed, the flux of nutrients and pollutants should be a top priority of an ecosystem-based management that needs to employ innovative socio-environmental approaches involving participatory, multisectoral, multidisciplinary, integrated and co-management efforts. The looming climate change, which may undoubtedly lead to further loss of biodiversity services, needs to be incorporated in the watershed modelling and management framework.