The urban growth intricately linked to the hydrological cycle outlines a crucial dynamic in the environmental transformations of cities. Utilizing the InVEST (Integrated Valuation of Ecosystem Services and Tradeoffs) Urban Flood Risk Mitigation model, we conducted hydrological modeling to assess the impact of urbanization on land use and land cover (LULC) changes and their subsequent effects on runoff generation in Itaperuna, Brazil, spanning the years 2015 to 2020. The analysis, performed across 17 urban sub-basins, highlights rapid urban expansion, notably in sub-basins 3 and 7, reflecting the city’s spatial dynamics and growth. Significantly, sub-basin 3 exhibited a 7.42% increase in runoff production capacity. The study meticulously documents changes in six LULC categories—water bodies, urban area, exposed soil, forest, natural pasture, and grassland vegetation—revealing that urban growth has directly amplified surface runoff in specific sub-basins, thereby impacting water resource management and flood prevention. Emphasizing the urgency of environmental conservation, especially in deforested basins, the findings hold substantial importance for urban planners and local authorities, offering relevant insights for flood risk mitigation and water security. Future research directions may explore additional facets, including water quality, advanced hydrological models, impacts on biodiversity and society, socioeconomic assessments of preventative measures, public policy considerations, and monitoring systems.