Impacts of artificial water level (WL) regulation on permanently submerged and intermittently submerged sediment physic-chemical properties and phosphorus adsorption–desorption behaviors were examined. Due to organic matter (OM) loss, median size (MS) and specific surface area (SSA) of sediment particles were significantly increased and decreased with increasing WL regulation velocities, respectively. Regardless of submerged sediment types, WL regulation decreased and increased the proportion of sediment particles with size smaller and bigger than 20μm, respectively. Film-diffusion was the rate-limiting step and physic processes dominated phosphorus adsorption. WL regulation greatly increased sediment amorphous iron oxides (Feox) and amorphous aluminum oxides (Alox) concentrations, which subsequently caused 2.03–390.75mg/kg improvement in Langmuir obtained maximal phosphorus adsorption capacity, and 25.81–50.00% decline in phosphorus adsorption buffering capability.