The irrigation system problem in South Kalimantan is removing pyrite from it. It is beacuse The flow pattern does not work well. This research is to study the flow patterns in handil irrigation system using SMS (Surfacewater Modeling System). The data are Barito River map, Alalak River map and the map of irrigation system with total area of study is ± 69,8 Ha. The manning roughness was calibrated using RMA2. The result of simulations shows that the irrigation canal of existing and normalization condition is not effective, because the flow pattern can not reach to the entire irrigation system. This is because the primary and secondary canals are too long. The tabat weir is an effective construction for maintaining the water level, so that the irrigation channel is not dry and prevent the pyrite comes to the top soil.