Phosphorus (P) is an essential element in the aquatic environment that is closely linked to river sediment dynamics. The effect of sediment on P has been widely recognized, but has been limited to specific scenarios without considering its relation to water quality management under different sediment scenarios. Water samples (1139 samples) collected from eight rivers across China were analyzed and a consistent comet-shaped relationship between sediment and dissolved P (DP), the component most directly impacting aquatic ecosystems, was observed. It indicated that in rivers with high sediment concentration (S), sediment has a strong controlling effect on P levels in water quality, but with decreasing S, this effect gradually diminishes and water quality is mainly influenced by P input. Extensive laboratory experiments were conducted and substantial differences in P concentrations were found across different methods, reaching up to two orders of magnitude. Some official methods showed significant uncertainties influenced by S and particle size, as confirmed by sediment settling theory, compromising accurate water quality assessment in rivers with high S. Among the methods considered in this study, filtering proved to be the most operationally feasible and effective in terms of its impact on water quality. These results have important implications for the assessment and management of P in aquatic water quality, as well as for the development of future environmental policies and regulations.