Abstarct: Checkdams are popular and frequently used structures in mountainous areas in order to preventing sediment erosion, slowing down and storing the surface water for planting, reforestation and also flood mitigation. From the flood control view point, checkdam configuration and their numbers throughout the watershed are very important factors to mitigate floods in downstream of rivers. A poor design of checkdams and their arrangement may not efficiently mitigate floods, but even may cause to intensify the flood peak discharges during rainfalls by synchronizing the surface runoff produced in upstream tributaries. In this paper, the effect of checkdams on flood characteristics was studied by a hydrological model and the best layout and number of checkdams on stream network was attained by coupling the hydrologic model with NSGA2 optimization algorithm. Hybrid model was then applied to two watersheds and optimal designs were derived for three design flood scenarios with 2, 5 and 10 years return periods, considering the “efficiency” and “checkdam cost” criteria. Experimental results show that optimal strategies can mitigate the flood peak discharges up to 70% with significantly lower costs or number of checkdams relative to a traditional design with a large number of checkdams in sub-watersheds presenting maximum 38% efficiency. This highlights the importance of developing and applying intelligent tools for design and site selection of checkedams throughout the watershed.