A 2-stage flood estimation and water quality decision support tool (DST) was developed, calibrated, and applied to a field site in south-eastern New South Wales (NSW) to simulate tidal restoration in a flood mitigation drain affected by acid sulfate soils leachate. The first stage of the DST employs a digital terrain map, geographic information tools, and measured water levels to calculate drain water overtopping due to tidal variations. Simulations using the GIS technique at the study site indicated that the primary drainage network can safely contain full tidal flushing (0.91 m AHD or a 58% increase), whereas at the same level the secondary drainage network overtops along relict drainage channels. The second stage of the DST simulates the change in drain water quality using an ion-specific program code written within the open interface PHREEQC program. The results from the water quality model were calibrated against laboratory titration tests. Drain water pH was shown to increase above 6.0, and soluble aluminium and iron concentrations decreased by 73% and 56%, respectively. The extent of water quality change is directly related to the ionic strength of the intruding water and the ion-specific reaction kinetics of aluminium, iron, and sulfate.