Abstract: The excessive phosphorus concentration in the upper reaches of the Qingshui River has seriously affected the water ecological security. In order to investigate the source, migration and transformation of total phosphorus, the annual total phosphorus flux, the inflow of exogenous sources and the release (or deposition) of endogenous sources in some sections of the Qingshui River and related waters from 2013 to 2016 were calculated. The results show that: the concentration of total phosphorus in the waters near the Xingrenqiao in the upper reaches of the Qingshui River is low and stable. The high total phosphorus in the middle reaches of Panghai-Jinping is due to the influx of high phosphorus water in the Chongan River, a tributary of the Qingshui River. The waters suffering more endogenous release of total phosphorus are the Gedong-Jinping section in the middle reaches, followed by the Baishi section; the area suffering the largest exogenous inflow of total phosphorus is the Chongan River. The inflow of total phosphorus from Xingrenqiao to Gedong section decreases year by year, but the inflow of total phosphorus from Gedong to Baishi section increases.