This paper reports on a mathematical model developed to simulate salinity intrusion in coastal waterways in South Eastern Coastal lowlands of Gold Coast (Australia), to neutralize acidity caused by pyrite oxidation. The model was used to predict the effect of salinity intrusion upstream of existing floodgates. Predictions of the model compared favourably with the field results. Intrusion of saline water can reduce pH of the upland water from 2.4 to about 6.0, while the salt levels remain low enough that it is not of concern to the landholders. Based on the computer predictions and experimental observations, it was concluded that the Nerang river flood mitigation system ought to be redesigned to allow controlled tidal water intrusion upland of the floodgates to neutralize acid leached from the groundwater. Such a structure would have to be constructed and installed in the creeks replacing existing one-way floodgates thereby allowing flow of saline water upland during inland tidal periods. In this manner, the saline creek water can neutralize much of the acidic water stored upland of the floodgates thereby reducing the ill-effect on fish and other estuarine communities and their habitats downstream following heavy rainfalls.