The Soil Water Assessment Tool (SWAT) was used for exploring the sources and retention dynamics of phosphorus nutrient in the river system of the Yong River Basin, China. The performance of the SWAT model was assessed. The retention dynamics of phosphorus nutrient in the river continuum and the factors contributing to those patterns were studied. The results showed that an average of 1828 tons of TP entered the river network of the Yong River Basin annually and in-stream processes trapped 1161 tons yr−1 of TP in the watercourse, which accounted for 63.5% of the annual TP inputs. The TP retention rates in the river network ranged from 3.08 to 63.43 mg m−2 day−1. An average of 666.9 tons of TP was delivered from the estuary to the East China Sea annually. The unit area riverine exports of TP ranged from 102.21 to 244.00 kg km−2 yr−1. The river network is a net sink for TP and is going through a phosphorus accumulation phase. The results confirm that the river system has a considerable phosphorus retention capacity that is highly variable on a spatiotemporal scale. Because of the cumulative effect of continued phosphorus removal along the entire flow path, the retention fractions of phosphorus removed from all streams at the basin scale is considerably higher than that of an individual river portion. The variations of hydrological regimes, water surface area, unit area inputs of phosphorus, and the concentrations of suspended sediments have a great influence on phosphorus retention.