Decreased water management systems and sea level rise cause inundation in the Katingan tidal agricultural lowland. Excessive and prolonged inundation can decrease rice production or even loss of rice land. A study was conducted to provide adaptive water management for controlling water levels in canals and rice crop fields inundation. For this purpose, a combined one- and two-dimensional unsteady flow method was used in HEC-RAS. The scenario of water level control uses sluice and flap gates in secondary canals. Under spring tide conditions, water level control with gates decreases the inundation area by 95.62%. Likewise, in the 25 and 50-year sea level rise scenarios, inundation decreased by 88.51% and 82.25%. In the spring tide condition, the duration of inundation is decreased from 3.5 to 0.9 days. Under 25 and 50-year sea level rise scenarios, the duration of inundation was decreased from 3.7 to 3 days and from 4.3 to 4.1 days. The use of gates significantly decreases inundation in the spring tide condition, but under sea level rise in 25 and 50-year, the depth and duration of inundation are still dangerous for rice crops; therefore, it is necessary to advance water management control for the sustainability of rice fields.