The water environmental capacity of alpine fragile rivers, constrained by hydrological-biogeochemical coupling processes, has long lacked robust quantitative investigations. Herein, we selected specific reaches of the Taohe River as the study area, leveraging the SWAT (Soil and Water Assessment Tool) model to simulate watershed runoff dynamics, and integrating the WASP (Water Analysis Simulation Program) model for analyzing riverine water quality indicators. A coupled SWAT-WASP water quality model was thereby constructed, accompanied by the establishment of a quantitative calculation framework for water environmental capacity, to assess the spatiotemporal patterns of water environmental capacity in the alpine watershed at the northeastern margin of the Qinghai-Tibet Plateau. Model simulations exhibited strong concordance with measured data, with correlation coefficients exceeding 0.6 for water discharge and runoff depth. Under Class Ⅰ water quality standards, the annual water environmental capacities for BOD, TP, and DO were 157.6, 2.067, and 221.8 tons, respectively; in contrast, TN required relaxation to Class Ⅳ standards, yielding an annual capacity of 50.38 tons. Spatially, the water environmental capacities of BOD, TP, and DO in the upstream section accounted for 9.9%~10.3% of those in the downstream, while temporally, their capacities in January (dry season) represented 10.1%~34.2% of those in July (wet season). These findings underscore the dominant roles of hydrodynamic conditions and seasonal hydrological drivers in alpine fragile watersheds, defining the sustainable development thresholds for such systems. With TN identified as the priority control factor, a spatiotemporally coordinated allocation strategy is proposed, offering a scientific foundation for adaptive water quality management in alpine fragile water source regions.