Riverine ecosystems are increasingly threatened by global changes that include drought, extreme weather events, and anthropogenic alterations to natural flows. The health of Australia’s longest and most important river system, the Murray-Darling, is dependent on the soils, microorganisms, and plant communities that underpin it. In submerged soils where iron (from soil minerals), organic material and sulfate (from groundwater salts) are available, sulfate reducing microorganisms produce sulfidic materials. These sulfidic materials are typically pyrite (FeS2); the accumulation of these materials leads to the formation of acid sulfate soils. If these materials are subsequently oxidised (e.g. due to draining), iron oxidising microorganisms enhance the production of sulfuric acid, which causes soil pH to decrease to <4. These are termed acid sulfate soils with sulfuric materials. The development of strongly acidic soil in altered landscapes reduces wetland productivity and water quality; it is a highly undesirable outcome. This project investigates the possible outcomes of wetland management (wetting and drying) on soil microbial diversity and community structure in acid sulfate soils. This was achieved via an extensive literature review, biochemical analyses of two wetland complexes, and DNA diversity analyses via Illumina Sequencing of the 27F-519R amplicon (16S; n = 24). Soil DNA analyses were conducted on freshly acquired and oxidised (8-12 weeks) samples from the Muthro Park and Spectacle Lakes wetland complexes to determine microbial diversity shifts caused by oxidation. The research has highlighted substantial knowledge gaps ranging from the ecologies of iron and sulfur cycling microorganisms through to best practice options for preventing sulfide accumulation and catastrophic oxidation of sulfidic materials. The findings from this study will inform management decisions on wetting and drying regimes in Murray-Darling wetland ecosystems.