Microbial communities play a critical role in biogeochemical processes in semi-arid floodplain wetlands. In this talk, we present the results of two recent studies undertaken for the Macquarie Marshes, south-east Australia that investigated the influence of historical inundation frequency on the relative abundance of soil microbes and the metabolism of carbon sources by planktonic microbes following inundation. We used high-throughput sequencing to identity dominant microbes, targeting the 16SrRNA gene and Biolog EcoPlates™ to assess microbial utilization of 31 carbon sources. Historical inundation frequency had contrasting effects on the relative abundance of two dominant phyla (Actinobacteria and Proteobacteria) and the metabolism of carbon sources was highest in the least historically inundated area, leading to a heterotrophic state in terms of planktonic metabolism. Our results indicate a spatial gradient of the floodplain microbial community structure and functioning along inundation frequency in semi-arid regions.