Wetlands in many inland catchments are being subjected to increasing salinity. To expand our limited understanding of how increasing salinity will alter carbon and nutrient dynamics in freshwater sediments, we carried out microcosm experiments to examine the acute effects of increasing salinity on the anaerobic cycling of carbon, nutrients (N, P, and S), metals (Fe and Mn), and microbial community structure in sediments from a non-salt-impacted freshwater wetland. Sediments were collected from a wetland on the River Murray floodplain, south eastern Australia and incubated with NaCl concentrations ranging from 0 to 100 mmol L⁻¹. Increasing NaCl concentration led to the immediate release of between about 80 and 190 μmol L⁻¹ ammonium and 235 to 3300 μmol L⁻¹ Fe(II) from the sediments, the amount released ‘increasing with NaCl concentration. Conversely, net phosphate release decreased with increasing NaCl concentration. The overall microbial community structure, determined from phospholipid fatty acid profiles, changed only at the highest NaCl loadings, with evidence of a decrease in microbial diversity. Bacterial community structure, determined by examining terminal restriction fragment length polymorphism (T-RFLP) of the bacterial 16S rRNA gene, showed little response to increasing NaCl concentration. Conversely, the archaeal (methanogen) population, determined by examining T-RFLP of the archaeal 16S rRNA gene, showed significant changes with increasing NaCl loading. This shift corresponded with a significant decrease in methane production from salt-impacted sediments and therefore shows a linkage between microbial community structure and an ecosystem process.