Reservoirs in Taiwan are inundated with nutrients that result in algal growth, and thus also reservoir eutrophication. Controlling the phosphorus load has always been the most crucial issue for maintaining reservoir water quality. Numerous agricultural activities, especially the production of tea in riparian areas, are conducted in watersheds in Taiwan. Nutrients from such activities, including phosphorus, are typically flushed into rivers during flooding, when over 90% of the yearly total amount of phosphorous enters reservoirs. Excessive or enhanced soil erosion from rainstorms can dramatically increase the river sediment load and the amount of particulate phosphorus flushed into rivers. When flow rates are high, particulate phosphorus is the dominant form of phosphorus, but sediment and discharge measurements are difficult during flooding, which makes estimating phosphorus flux in rivers difficult. This study determines total amounts of phosphorus transport by measuring flood discharge and phosphorous levels during flooding. Changes in particulate phosphorus, dissolved phosphorus, and their adsorption behavior during a 24-h period are analyzed owing to the fact that the time for particulate phosphorus adsorption and desorption approaching equilibrium is about 16 h. Erosion of the reservoir watershed was caused by adsorption and desorption of suspended solids in the river, a process which can be summarily described using the Lagmuir isotherm. A method for estimating the phosphorus flux in the Daiyujay Creek during Typhoon Bilis in 2006 is presented in this study. Both sediment and phosphorus are affected by the drastic discharge during flooding. Water quality data were collected during two flood events, flood in June 9, 2006 and Typhoon Bilis, to show the concentrations of suspended solids and total phosphorus during floods are much higher than normal stages. Therefore, the drastic changes of total phosphorus, particulate phosphorus, and dissolved phosphorus in rivers during flooding should be monitored to evaluate the loading of phosphorus more precisely. The results show that monitoring and controlling phosphorus transport during flooding can help prevent the eutrophication of a reservoir.