Tonle Sap Lake (Cambodia), a classic example of a “flood pulse” system, is the largest freshwater lake in SE Asia, and is reported to have one of the highest freshwater fish productions anywhere. During the dry season (November–April) the lake drains through a tributary to the Mekong River. The flow in the connecting tributary completely reverses during the wet monsoon (May–October), adding huge volumes of water back to the lake, increasing its area about six fold. The lake is likely phosphorus limited and we hypothesized that groundwater discharge, including recirculated lake water, may represent an important source of P and other nutrients. To address this question, we surveyed hundreds of kilometers of the lake for natural 222Rn (radon), temperature, conductivity, GPS coordinates and water depth. All major inorganic nutrients and phosphorus species were evaluated by systematic sampling throughout the lake. Results showed that there were radon hotspots, all at the boundaries between the permanent lake and the floodplain, indicating likely groundwater inputs. A radon mass balance model indicates that the groundwater flow to Tonle Sap Lake is approximately 10 km3/yr, about 25% as large as the floodwaters entering from the Mekong River during the wet monsoon. Our results suggest that the groundwater-derived dissolved inorganic phosphorus (DIP) contribution to Tonle Sap is more than 30% of the average inflows from all natural sources. Since the productivity of the lake appears to be phosphorus limited, this finding suggests that the role of groundwater is significant for Tonle Sap Lake and perhaps for other flood pulse systems worldwide.