Estuarine acidification, caused by disturbance of acid sulfate soils (ASS) is a problem that affects many estuaries in eastern Australia. ASS outflows have low pH and elevated concentrations of metals, principally iron and aluminum. Most production of Sydney rock oysters Saccostrea glomerata occurs in estuaries along the Australian east coast and estuarine acidification has been implicated in localized declines in oyster production. Estuarine areas recurrently impacted by estuarine acidification have higher levels of oyster mortality and reduced oyster growth compared with sites that are not acidified. Two laboratory experiments were conducted to investigate reasons for poor oyster production at sites exposed to ASS-affected waters. Behavioral response, soft tissue lesions and filtration rates of S. glomerata when exposed to ASS-affected waters were examined. It was found that ASS-affected water altered oysters’ valve movements and significantly reduced filtration rates at pH 5.5. Acidic treatments (pH 5.1) containing 7.64 mg L−1 of aluminum or ASS-affected water caused changes in the mantle and gill soft tissues after short-term (6 h) exposure. Degenerative effects were also caused by iron contained in ASS-affected water. Iron precipitates accumulated on the gills and mantle and were observed in the stomach, intestine, digestive tubules and rectum. Results from this study highlight the rapid deleterious effects of reduced pHs to oysters and the impacts of iron and aluminum contained in ASS-affected waters.