The eutrophication of shallow lakes has become a global environmental issue. Phosphorus (P) is a key driver of lake eutrophication, and its distribution within sediments, as well as the transformation among its different fractions, directly influences the potential for internal P release and the trajectory of ecological restoration. While existing studies predominantly focus on internal phosphorus (P) release in shallow lakes, the long-term alterations in sedimentary P speciation driven by eutrophication and the underlying ecological feedback mechanisms remain poorly understood. In this study, 37 shallow lakes in the Eastern Plain of China were selected as research subjects. Based on sediment core records and combined with contemporary physicochemical water quality observations, we reconstructed the centennial evolutionary history of P fractions in lake sediments and explored their environmental implications. The results indicate that eutrophication has led to an increase in algal biomass, leading to an increase in the content and proportion of high-release-risk active phosphorus in surface sediments, alongside a decrease in the content and proportion of relatively stable calcium-bound phosphorus (Ca-P). Furthermore, the ratio of Ca-P to calcium (Ca) continuously decreased over the time series, indicating a gradual weakening of phosphorus fixation processes associated with calcium carbonate. These processes include the substitution of phosphate ions (PO43-) for partial carbonate ions (CO32-) within the crystal structure of calcium carbonate (CaCO3), as well as the formation of insoluble calcium-phosphate minerals on the surface or within the interior of CaCO3 crystals. This further suggests that the accumulation capacity for inert phosphorus in shallow lake sediments may be impaired under eutrophic conditions. This study concludes that the elevated proportion of labile P in sediments will exacerbate the risk of internal P release and intensify the positive feedback loop of the turbid water state, thereby making the restoration of lake ecosystems significantly more difficult.