Floods cause considerable damages worldwide and mitigation of their adverse effects through effective protection measures is needed. Along with the commonly applied “grey” infrastructure, “green” measures that can offer additional benefits, such as ecosystem services, are increasingly being considered lately. While the recent research tendencies are focused on the effectiveness and the value of green measures in urban areas, this paper presents a comprehensive financial evaluation of green and grey flood mitigation scenarios for a smaller rural watershed. A micro-scale damage model that builds on the hydrodynamic modeling of hazard, detailed asset identification, and damage assessment is presented and applied for evaluation of benefits from various flood mitigation measures in the Tamnava watershed in Serbia. Four scenarios are considered: (1) existing flood protection system; (2) green scenario involving new detention basins; (3) grey infrastructure enhancement by rising of the existing levees and diverting flood discharges; and (4) green-grey scenario that combines scenarios (2) and (3). The benefits (loss reduction) are the greatest with the green scenario and marginally higher with the combined green-grey scenario. The results suggest that for small rural watersheds, a holistic, integrative approach that includes both types of infrastructure can provide the most effective flood risk mitigation.