Coastal environments in Australia are under development pressures. Human settlement encroaches on disease vector salt marsh mosquito breeding areas that are underlain by potential acid sulfate soils (PASS). Altering the hydrology by runneling solves the mosquito problem but may lead to acid sulfate problems. Appropriate analytical tools can assess the risk to the environment. The objective of the research was to compare three methods of assessing PASS. The study area was a low-lying intertidal subtropical salt marsh that was being considered for runneling. The results indicated that using field pH and field peroxide pH (and the relationship between these), and also the peroxide oxidation-combined acidity and sulfate (POCAS) test, appeared to overestimate the potential acidity. This was because the source of acidity in the intertidal salt marsh includes a large organic content, which is not a major environmental concern. The chromium-reducible sulfur test, which is not affected by organic content, was found to provide the most appropriate assessment, and is recommended for use in highly organic salt marshes.