We have investigated the relationships between Mekong River/Tonle Sap hydrology, the dissolved and particulate phosphorus (P) cycle and aquatic productivity (measured via chlorophyll-a) in the Tonle Sap/Mekong River system. This involved measurements in the contiguous Mekong Region countries Thailand, Laos, and Cambodia. Emphasis was placed on Tonle Sap Lake, the largest and most productive lake in SE Asia. We hypothesized that P is the limiting nutrient in this system, and feel that its sources and transformations have not previously been well described. We further hypothesized that the P cycle is intimately related to the hydrologic cycle of this flood pulse system. Geochemical measurements and modelling were used to determine the sources of P to the lake and its relationship to the hydrologic stage of the river and lake. We were particularly interested in evaluating the role of groundwater to the P cycle, an area that has been largely ignored. Our approach consisted of combining continuous measurements of radon, a groundwater tracer, with detailed P speciation measurements. The overarching objectives were to assess and model nutrient and productivity impacts in response to climate change, dam construction or other development activities in the Mekong River basin that will affect downstream river flow.