Under the influence of global warming, the temperature of lakes and rivers in the Qinghai-Xizang Plateau has increased significantly, and the change is closely related to the breeding of aquatic organisms. However, there are few studies on the water temperature at the estuary of rivers, which is an important place for the migration and spawning of Gymnocypris przewalskii in Qinghai Lake, and the influence of water temperature change on the spawning of G. przewalskii is still unclear. Therefore, this study is based on the observation data of Gangcha Meteorological Station, China Meteorological Forcing Dataset (CMFD), European Centre for Medium-Range Weather Forecasts Reanalysis v5-Land (ERA5-Land) and Coupled Model Intercomparison Projects 6 (CMIP6). The Fresh water Lake Model (FLake Model) is used to simulate the water temperature at the estuary of Buha River, the largest tributary of Qinghai Lake, and evaluate its applicability. It also discusses the superiority of reanalysis and CMIP6 multi-model data to drive the collection of simulated historical water temperatures (1981-2014). The evolution and causes of water temperature under three scenarios in the future period (2024-2100) are estimated. The results show that: (1) Average water temperature simulated by CMFD and ERA5-Land was better than that of the single model, and the accuracy of the simulation results was better in both short and long terms, of the average simulated water temperature of CMIP6 multi-model was better than that of a single model, which reproduced the simulated water temperature of reanalysis data set effectively. (2) In the future, the water temperature at the estuary of the Buha River may increase significantly with the increase of emission intensity. The meteorological factors that were positively correlated with the water temperature are air temperature, specific humidity, downward long wave radiation and downward short wave radiation from the largest to the smallest, while the wind speed was negatively correlated is; except for the downward short-wave radiation of the long-term high emission scenario (SSP585), the meteorological factors of the others all passed the 95% significance test. (3) In the recent period (2024-2040), the water temperature under the three scenarios may elevate slightly, increased compared with the historical period, and there is little difference between the water temperatures. The spawning window period of G. przewalskii is slightly shortened, and the rising water temperature will have a slight impact on the spawning of G. przewalskii. In the middle period (2041-2060), the water temperature of the three scenarios increased further, and the difference between the water temperatures gradually appeared. The spawning window period of G. przewalskii was obviously shortened, and the rising water temperature had certain harm to the spawning of G. przewalskii. In the long term (2081-2100), the water temperature difference between the three scenarios is more significant, and the rise rate of SSP126 and SSP245 scenarios slows down. In the SSP585 scenario, the rate of water temperature rise was still accelerated, and the continuous rise of water temperature resulted in a significant shortening of the spawning window period of G. przewalskii, which limited the spawning activities of G. przewalskii to a certain extent.