Sumbangtimun Village and Kandangan Village, in the lower part of Bengawan Solo River, are regularly flooded almost every year. These flood prone area are situated in the river meander with low natural levee. Losses due to flood damage were estimated to reach 2.5 billion rupiah in the year 2007/2008 with the greatest losses from agricultural sector. These losses were caused by flooding that comes early before the harvest time. Surround dike to prevent flood inundation is recommended by the river authority. Regarding different land uses, i.e. rice fields, tree crops plantation, settlement, with different inundation tolerant, a set of mini polder is proposed to overcome the problem of inundation and its water management. The polder system is attributed by surrounded dike, local drainage system and pond retention with or without pumping system. The mini polder system that is equipped with lateral gate as flood control structure is proposed to solve the problem of inundation in the agriculture and settlement areas. Hydraulic mathematical models (HEC-RAS and Pond Pack) for simulating flow characteristics in the flood prone area are employed to determine the design of an appropriate mini polder system and its operational procedures.