Rice fields in the Katingan tidal lowlands are inundated due to spring tides and extreme rainfall. Excessive inundation in the rice fields causes crop failure. Therefore, the study was conducted to analyze the use of water gates in the secondary canals for controlling the inundation. The unsteady flow simulation boundary conditions are the upstream discharge with a return period of 5 and 25 years and measured tidal. The water flow is controlled by closing the sluice gates at the water level elevation of +3.50 m, and flap gates close during high tide and rainfall. This research shows that controlling the water flow by gates decreases the water level and inundation area. Under rainfall with a return period of 5 years, the inundation area decreased by 79.03 %, and the maximum water level decreased by 0.14 m. In the rainfall with a return period of 25 years, the inundation area decreased by 75.31%, and the maximum water level decreased by 0.11 m. The water gates’ operation incompletely decreases the inundation and water level beneath rice crops’ threshold inundation depth and duration. Therefore, there is a need for additional water control to optimize the decrease of inundation in the rice fields.