Water is fundamental to all ecosystem services, yet a comprehensive assessment and economic valuation of total water contributions to ecosystem service production using a fully integrated groundwater–surface water model has not previously been attempted. Quantifying the multiple ecosystem services affected by water use requires an analytical framework that explicitly captures both subsurface and surface water resources. However, incorporating subsurface water into ecosystem service evaluations remains a recognized scientific challenge. In this study, the fully integrated model HydroGeoSphere (HGS) was applied to simulate subsurface water, surface water, and transpiration (green water use), combined with an economic valuation approach to assess ecosystem services over an 18-year period (2000–2017) in the South Nation Watershed (SNW), a 3830 km² mixed-use but predominantly agricultural watershed in eastern Ontario, Canada. Using green water volumes generated by HGS and ecosystem service values as inputs, the marginal productivity of water was estimated at CAD 0.26 m⁻³ (2022 dollars). Results show that green water values peaked during drought years, with the 2012 extreme drought reaching CAD 424.7 million. In wetter years, green water values were as low as CAD 245.9 million, with the 18-year average at CAD 338.83 million. Since subsurface water is the sole contributor to green water supply, it plays a critical role in sustaining ecosystem services during drought conditions. This study provides new insights into the economic contributions of subsurface water and its role in ecosystem resilience, while proposing an improved methodology for watershed-based ecosystem service management and valuation.