Phosphorus(P), as a limiting and vital macronutrient in global freshwaters, circulates mainly with sediment through rivers. In this paper, we analyzed and summarized the regime of P and its variations that induced by dams burgeoning in the upper Yangtze River basins in recent decades. We revealed that more than 91% of the P flux is in particulate form, among which the potential dissolvable bio-active P (BAP) can exceed the total load that discharged from the riparian basins. The P is closely correlated with sediment and we estimated that reservoirs have by more than 3 quarters of it sequestrated. Previously, the BAP was mostly absorbed by sediment and flushed by floods to the estuary, where it supported a flourishing saline bio-ecosystem at the same time, with minor residuals in the lowland freshwaters. However, this nature endowed regime was upset by the sequestration of reservoirs that reallocated reversely the background P as inner pollution for the freshwater corridors and snatched the inherent nutrient for ecosystem of the estuary. Moreover, the resultant clear-stream lost its buffering effect that sediment regulates P and the lowland freshwater becomes more vulnerable with lowered environmental capacity. Accounting for the actual eutrophic status, the pool elevated dissolvable P level may also add potential risks in stimulating harmful algal blooms and hypoxia to the Three Gorges Reservoir and others. On another hand, in order to keep a basin wide consistent monitoring and criterions in P control from water to water and we can evaluate the harmful effect of dams more objectively, we recommend urgently to correct the present P analysis regulation, which requires P extraction from water samples after 30 min settling, that can lose a significant amount of P. Finally, we proposed to restore the downstream biogenic-substance and eliminate the in-pool accumulating P contamination through successive slurry dredging from reaches in front of the dams.