The Tonle Sap is the largest wetland in South-east Asia and the heart of the largest inland fishery in the world. Its unique flood pulse system and annual flow reversal is a hotspot for biodiversity and productivity, as well as an essential habitat for many endangered fishes and birds. Despite predicted changes to the wetland's hydrology due to climate change and hydropower development in the Mekong, the consequent impacts on the fauna of the lake are poorly understood. A spatial modelling framework was developed to simulate the impact of potential scenarios of change using relationships between fauna and biophysical characteristics. Potential impacts on 61 animal species with documented nutritional, conservation or ecological value were examined. A large number of species rely on gallery forest to provide important habitats for their life history, yet this area is likely to be highly impacted by permanent inundation. There is a strong synchronicity between life histories and the flood pulse; consequently continued hydrological disruptions will have a significant impact on ecosystem dynamics, imposing further challenges to conservation. Protecting areas that may become suitable for gallery forests and shrublands under a modified flood regime will be crucial to management planning and the maintenance of a diverse and healthy ecosystem.