While there is a wealth of research on the water quality improvement effects of lake ecological restoration projects, a systematic assessment of the dynamic changes in endogenous pollution in sediments and the mechanisms of nitrogen and phosphorus release is lacking. In particular, the seasonal characteristics of nutrient release at the sediment-water interface after ecological restoration of eutrophic lakes in the plateau region remain unclear. This study takes Dapokou, a typical eutrophic water area in the Caohai Lake of Dianchi Lake, as the research object. By comparing the water environment characteristics, sediment nitrogen and phosphorus occurrence forms, and interface release fluxes in the ecological restoration area and the unrestored area during the rainy season (peak growth period of submerged plants) and the dry season (decline period of submerged plants), the study systematically elucidates the spatiotemporal distribution characteristics of nitrogen and phosphorus in the overlying water-sediment system and the seasonal evolution of interface release fluxes in the ecological restoration area. The results show that ecological restoration improved the quality of the overlying water environment, with the water structure exhibiting a transformation from algal to grass-like patterns. During the rainy season, the total nitrogen (TN) and total phosphorus (TP) concentrations in the restored area decreased by 53.9% and 43.2%, respectively, compared to the unrestored area, while transparency (SD) significantly improved, and dissolved oxygen (DO) returned from supersaturation to normal levels. Regarding sediment occurrence, the remediation area exhibited differentiated evolutionary characteristics: total sediment nitrogen (STN) was significantly reduced by about 50% compared to the unremediation area, and convertible nitrogen (TTN) accounted for only 0.01%–0.02% of total nitrogen, with nitrogen mainly in stable form; however, bioavailable phosphorus (BAP) was enriched in the surface layer of the remediation area (reaching 468.72–534.35 mg/kg), forming a high potential releasable phosphorus reservoir. Regarding nitrogen and phosphorus release characteristics, the release flux at the sediment-water interface exhibits a clear seasonal shift: during the rainy season, when submerged plants are thriving, the interface is dominated by net adsorption, with a sediment-phosphorus (SRP) release flux of -1.08 mg/(m2·d). During the dry season, the decomposition of plant remains alters the sediment microenvironment, significantly increasing the interfacial release flux. At some sites, the ammonia nitrogen (NH4+-N) release flux reaches 86.31–91.53 mg/(m2·d), more than seven times that of the unrestored area, and SRP also shifts to a release state. In summary, the Dapokou ecological restoration project demonstrates improved water quality and net adsorption at the interface during the plant growth period, but there is a risk of nitrogen and phosphorus re-release due to remains decomposition during the dry season. Given the significant fluctuations in water levels and the concentrated seasonal decline of vegetation in shallow plateau lakes, submerged plant restoration measures should be combined with management methods such as dry season debris removal, water level regulation, and bottom sediment oxidation maintenance to control the intensity of seasonal endogenous release and provide a scientific basis and engineering reference for the treatment of endogenous pollution in Dianchi Lake and similar plateau lakes.