The driving mechanisms behind the differential shrinkage of lakes on the Inner Mongolia Plateau under similar climatic and anthropogenic pressures remain unclear, hindering targeted ecological restoration. This study investigates two adjacent lakes, the bowl-shaped Daihai (DH) and the dish-shaped Huangqihai (HQH), to reveal the dominant role of lake basin topography. Integrating remote sensing, field data, and numerical models, we analyzed the hydrological evolution of both lakes from 1987 to 2008. Key findings: (1) HQH's shallow, dish-shaped basin is more sensitive to hydrological changes than DH's deeper, bowl-shaped basin; (2) For an equivalent decline in the regional groundwater table, HQH's groundwater recharge area (GRA) decayed at 2.01 times the rate of DH's, and its groundwater recharge (GWR) loss was 2.10 times greater; (3) HQH's shallow morphology triggered a vicious cycle of shrinking recharge area and decoupling of its recharge system, accelerating desiccation, whereas DH's bowl structure demonstrated greater resilience. These results demonstrate that basin morphology critically modulates groundwater recharge, explaining divergent shrinkage trajectories and highlighting the need for morphology-specific conservation strategies in arid regions.