The Tonle Sap is the largest and most important natural wetland in Southeast Asia. It covers an area of more than 15,000 km2 with a unique mosaic of natural and agricultural floodplain habitats that coexist with the largest fishery in the Mekong Basin. Accelerating hydropower development and climate change, however, are altering the Mekong’s hydrology, which could negatively affect downstream ecosystems. The Tonle Sap is facing a two-fold problem. First, the link between its hydrology and ecosystem properties is not well understood. Second, potential ecological changes caused by future hydrological disruptions related to hydropower and climate change are unknown. Thus, the main objective of this thesis was to quantify how alterations to the Mekong hydrology could affect the Tonle Sap ecosystem. The following studies were performed to addressed the objective: (1) an assessment of landscape patterns using geographical information and remote sensing tools; (2) an assessment of habitat patterns based on field surveys of water, vegetation, and soils; (3) ecosystem function modelling to simulate net primary production (NPP) as a function of water quantity, sediments, and habitat type; and (4) fauna habitat modelling linking the results from the assessment of landscape patterns to fauna species. The assessment of landscape patterns revealed a distinct relationship between inundation and vegetation. Habitats in the Tonle Sap were divided into five groups based on annual flood duration, as well as physiognomic factors and human activity: (1) open water, (2) gallery forest, (3) seasonally flooded habitats, (4) transitional habitats, and (5) rainfed habitats. Large habitat shifts could occur as a result of hydropower development scenarios by the 2030s; areas optimal for gallery forest could decrease by 82% from baseline conditions, whereas areas of rainfed habitats could increase by 10-13 % (813-1061 km2). The assessment of habitat patterns demonstrated that despite the complexity and intense human use of this ecosystem, the flood-pulse is the underlying driver of habitat characteristics by (1) determining inundation depth and duration; (2) creating the main soils gradient; (3) limiting the area cleared for agriculture; (4) influencing vegetation structure and water quality; and (5) shaping the composition of plant species. The ecosystem function model was used to estimate a reduction of 9-39% in annual NPP caused by different scenarios of hydropower development and/or climate change during 2032-2042. Cumulative impacts from hydropower would disrupt NPP to a greater extent than climate change. The fauna habitat model revealed that species richness was greatest in the gallery forests and seasonally flooded habitats. Animals that permanently reside in or that rely on these habitats to complete essential life-history stages would be the most affected by future changes. This thesis provides the first quantitative formulation that directly links fundamental components of the Tonle Sap ecosystem to its flood-pulse hydrology. It also provides a comprehensive assessment of the impacts of expected hydrological alterations. Hydropower is expected to bring more abrupt and distinct ecological alterations than climate change in future decades. Relative aerial changes to the gallery forests are expected to be greater than in other habitats. A decline of the Tonle Sap’s ecosystem services will occur if appropriate measures are not implemented. These measures include mitigating hydropower alterations, conserving natural habitats in areas that are likely to remain hydrologically undisturbed, restoring natural habitats in projected areas for optimal growth, and optimizing agricultural practices in the floodplain. Research findings from this thesis focused on the Tonle Sap, but given the fundamental commonalities between this system and other large floodplains, the information presented is highly informative to other large flood-pulse driven systems around the globe.