Public concern about the use of chemicals for mosquito control in coastal Australia has lead to the development of physical habitat modification methods that aim to reduce mosquito populations to acceptable levels. Habitat modification methods include runnels (depth < 0.30 m) and ditches (depth > 0.50 m). During excavation for habitat modification, a risk of exposure of acid sulfate soils may exist. Acid sulfate soils are soils that contain iron sulfides, in particular pyrite (FeS2), and produce sulfuric acid when exposed to air. These soils occur predominantly in coastal lowland areas that are also prime mosquito breeding habitats. The paper discusses the problem and illustrates the application of survey methods that facilitate wise decision making and management of intertidal wetlands.