The Kongque River Basin on the northeastern Tarim margin comprises the Kaidu River–Bosten Lake–Kongque River system, a representative mountain–oasis–desert complex in an arid environment. Observations show significant warming at ~0.027 °C yr⁻1 (1960–2010), advancing snowmelt, strengthening and advancing the spring freshet, and raising annual runoff in recent decades, while increasing dry-season shortage risk. ICESat-1/2 altimetry indicates Bosten Lake fell by ~0.37 m yr⁻1 during 2003–2009 (≈ −2.63 m total), then partially rebounded at ~0.06 m yr⁻1 during 2009–2020, yielding a net decline of ~0.58 m from 2000 to 2020. Downstream aridity remains extreme (precipitation <50 mm yr⁻1, evaporation >1400 mm yr⁻1), sustaining moisture deficits, irrigation pressure, and groundwater-overdraft risk. Projections (CMIP6) suggest that despite continued warming and modest precipitation increases, annual runoff will decrease by ~3.42 m3 s⁻1 decade⁻1 (RCP4.5) to ~7.20 m3 s⁻1 decade⁻1 (RCP8.5) due to enhanced evapotranspiration. These shifts amplify long-term hydrological variability and uncertainty, reinforcing the chain “warming → hydrological change → oasis carrying capacity → desert expansion.” Safeguarding hydrological security and sustainable oases will require optimized allocation, water-saving agriculture, integrated lake–river management, and ecological flow releases.