This chapter describes phosphorus dynamics in Tonle Sap Lake (TSL) based on a two-dimensional phosphorus dynamics model, including the major processes of horizontal advection–dispersion, internal loading, sedimentation, and the input from atmosphere, villages on the water, and tributary rivers of the lake. The calibrated model estimated that the total external total phosphorus (TP) influx from the tributaries and villages was 155 ton/month and 738 ton/month in the dry season and in the rainy season, respectively, from 1999 to 2003. In contrast, only 123 ton/month of TP flowed out from TSL in the dry season and 121 ton/month in the rainy season, indicating the removal of most of TP in the lake. The monthly water surface area was mostly mesotrophic (>79%). Noticeably, the eutrophic area expanded from 1.9% in November to 8.2% in May due to high concentration of tributary inputs and low net settling during the low-water period. The proposed model helps us understand the spatiotemporal changes in phosphorus dynamics in the lake.