Rapid urbanization has intensified challenges in urban water management, highlighting the growing importance of sponge city development. However, at present, the unique role of groundwater aquifers in regulating the water cycle process has been ignored, and overly simplistic construction methods are relied on. To address these limitations, this study introduces an integrated spatial optimization framework for urban-scale sponge ecosystems by coupling hydrodynamic modeling, ArcGIS-based spatial analysis, and Monte Carlo simulation. The framework systematically incorporates surface water depth, formation lithology, and groundwater depth to construct a comprehensive evaluation system for sponge ecological suitability. Shenzhen serves as the empirical case to demonstrate the framework’s applicability. Surface water depth is quantified using the Finite-Volume Community Ocean Model (FVCOM), while groundwater conditions are assessed through a calibrated groundwater model, thereby improving the scientific precision of ecological suitability evaluation. Leveraging GIS and Monte Carlo simulation, the study develops a streamlined yet robust methodology for optimizing the spatial configuration of sponge ecological infrastructure. Building on ecological redlines and protected areas, a landscape ecology–oriented matrix–corridor–patch analysis is applied to delineate ecologically suitable zones. Tailored planning and management strategies are subsequently formulated for each zone based on its ecological attributes. The findings offer methodological advances for sponge ecosystem construction and contribute to enhancing urban climate resilience and adaptive capacity under accelerating environmental change.