Reservoir water level regulation induces intricate processes of phosphorus (P) migration and release within the water-level fluctuation zone (WLFZ). These dynamic interactions pose significant challenges for effective pollution management strategies. This study focused on two typical tributary WLFZs (narrow gorges type and wide river type) in Three Gorges Reservoir (TGR), aiming to quantify P sources and assess their release potentials across two operational periods. Results showed that the deposition of suspended particulate P (SS-P) transported from the upstream was the dominant P source in the two WLFZs during the low water level period (August 2022). During the drainage period, the main P source of the ‘narrow gorges type’ WLFZ was P loss from slope soil above the WLFZ, but the ‘wide river type’ WLFZ had a mix of P sources, including P loss from slope soil, SS-P depositions from the TGR backwater and the tributary upstream. Among the three P sources, the slope soil source exhibited a relatively higher degree of P saturation (DPS) values (0.5–18.8%), indicating a greater potential for P release. Given that P loss from slope soil is the primary P source in the WLFZs during the drainage period, which coincides with the spring plowing season, it is crucial to implement measures to prevent P loss from slope soils to safeguard water quality in the TGR.