This study aims to understand the flow and water quality behaviour in response to the combination of rainfall and tides in the Dadahup Irrigation Area. Rainfall and tides have a strong influence on the Dadahup Irrigation Area. The impact of floods and droughts which hit the area in recent years changed its water quality because of salinity intrusion and the presence of pyrite in the irrigation area. The existing gates and levees along the main primary channel cannot fully regulate the water level on the other channels and on the paddy fields. This condition has resulted in crop failure in several places. Parameters of flow and water quality data such as rainfall, water level, pH, and salinity were measured from an newly installed telemetric monitoring system. A sampling period was selected in which both rainy and dry conditions were present. In that period, tides also oscillated the water level. Hydraulic simulations will analyze the hydrodynamic condition along with the observation results and will describe the flow profile and water quality changes. Simulations show that a high-intensity rainfall can immediately raise water levels in the main primary channel, and it impacts increasing pH and decreasing salinity.