The Sesan, Srepok and Sekong river basin (3S) is one of the Mekong’s most important tributary basins. The 3S rivers rise in Lao PDR and Vietnam and flow through Cambodia where they join before discharging to the Mekong. We assessed the status of the 3S river basin using the Freshwater Health Index (FHI), which measures a range of ecological health, ecosystem service delivery and resource governance metrics. Assessed as of December 2016 we used a combination of real and modeled data and stakeholder surveys to measure the basin’s capacity to sustainably provide ecosystem services. Ecosystem Vitality and Ecosystem Services achieved scores of 66 and 80 respectively out of a possible 100, whilst Governance & Stakeholders scored 43. Thus, the 3S provides the desired ecosystem services, but there are signs of ecological and hydrological stress, and weak capacity to cope with rapid change. Stakeholder engagement is an important component of completing and FHI assessment and we engaged with the IUCN’s 3S Bridge stakeholders group which comprises government officials, academics and NGO representatives from the three countries. By focusing on a common indicator framework this multinational stakeholder group was gained an appreciation of the 3S’s current health and future management challenges. The FHI assisted the group identify data deficiencies and made the 3S’s ecosystem-human-water dynamics more understandable. By establishing a common indicator framework, we will use the results to engage stakeholders in further exploring the FHI metrics and using them to develop a series of water resource management thresholds.