The development of a multidimensional phosphorus dynamic model for lake floodplain systems is still limited due to its complex hydrodynamics and environmental processes, which constrains our understanding and environmental management on eutrophication. Therefore, we developed a horizontal two-dimensional hydrodynamics-based phosphorus model and applied it to understand the phosphorus dynamics in the Tonle Sap Lake, a large tropical lake–floodplain system in Cambodia. This phosphorus dynamic model is based on a hydrodynamic model (local inertial model) and integrates the major phosphorus processes in the lake and the phosphorus inputs from tributaries and floating villages. The phosphorus dynamic model was applied to the period from September 1999 to December 2003 for elucidating the total phosphorus balance and the spatiotemporal distribution of its concentration. The model reproduced the seasonality of total phosphorus concentration with its root mean square error of 12 and 16 µg/L for the calibration and validation periods, respectively. During 1999–2003, the lake was in a mesotrophic to eutrophic state, whereas the average eutrophic area expanded from 8.0% in October to 45.3% in May, when the inundated area was reduced, due to a relatively high internal loading and the high concentration of tributary inputs. In addition, the model estimated that most of the external total phosphorus loading was settled down and the internal processes play an important role in phosphorus dynamics in the Tonle Sap Lake. As presented, the model analysis integrating hydrodynamics and internal processes substantially helps us understand the spatiotemporal dynamics of phosphorus in the lake–floodplain systems.