Oxidation of sulphide minerals in acid sulphate soils has acidified a substantial part of the low-lying coastal land in Australia. Such sulphides, including pyrite (FeS2) formed thousands of years ago during saline inundation of soils rich in iron. They do not pose a serious concern when submerged by the water table, because this prevents atmospheric oxygen reacting with the pyritic layer. However, flood protection of low-lying coastal land through the installation of deep surface drains has caused a general lowering of the water table elevation, that in turn has exposed the pyritic layers to atmospheric oxygen. High rainfall following droughts causes acid pollution of the surrounding flood mitigation drains, creeks and river systems. Large ground areas are affected by the transport of acid constituents during seepage. One way of controlling new acid production is through the installation of weirs in the flood mitigation drains in order to raise the water table elevation. In this paper, the acid pollution in New South Wales is reviewed, and the effect of groundwater elevation is examined. Relationship between acid production and groundwater table is examined. Mathematical models are developed to simulate acid production and transport, and two groundwater management regimes are examined. Weir based control of the groundwater table is shown to be successful in controlling acid production.