Rapid urbanization, increasing impervious surfaces, and land-use changes can disrupt natural hydrological processes and increase runoff and urban flood risk. Urban ecosystems, green spaces, and permeable surfaces can reduce runoff and flood impacts by enhancing infiltration, absorption, and water retention. This study aimed to assess the spatial and temporal changes in the urban flood-risk reduction ecosystem service in Baqubah, Iraq, using the Urban Flood Risk Mitigation (UFRM) model under a 25-year return-period rainfall event. The UFRM model from the InVEST suite, version 3.12.0, was applied to three temporal periods, 1364, 1384, and 1404, and rainfall durations of 15, 30, and 45 minutes. Input data included the watershed boundary, rainfall, land use and land cover, hydrologic soil groups, biophysical parameters, built infrastructure, and flood-damage information. The results showed an increasing trend in runoff-generation potential from 1364 to 1404, with stronger responses under longer rainfall durations. Under the 45-minute scenario, the dominant runoff range increased from approximately 10–50 mm in 1364 to about 60–150 mm and higher in 1404. Runoff absorption and retention capacity also showed spatial and temporal variation. Moreover, the economic value of the flood-risk reduction ecosystem service shifted from low and moderate classes in 1364 toward high and very high classes in 1404. Overall, the findings indicate that flood-risk reduction in Baqubah is a dynamic ecosystem service influenced by land-use and land-cover changes, hydrological characteristics, and rainfall duration. Protecting permeable surfaces, expanding green spaces, and implementing green infrastructure and nature-based solutions can contribute to sustainable urban flood-risk management.