Inundation frequency is one of the key environmental drivers that determine the structure and function of floodplain soil microbial communities. In this study, we examined the proportional abundance of Cyanobacteria and other dominant microbes in semi-arid floodplain soils, specifically from the Macquarie Marshes, south-east Australia, to determine whether historical inundation frequency has a significant effect on their abundance and spatial distribution. We used high-throughput sequencing to estimate the proportional abundance of the soil Cyanobacteria and other dominant microbes, targeting the bacterial 16S rRNA gene. Linear regression (generalised least-squares) models accounting for spatial autocorrelation showed that historical inundation frequency had no significant effect on the proportional abundance of Cyanobacteria. However, inundation frequency had a significant positive effect on the proportional abundance of Proteobacteria and a significant negative effect on the proportional abundance of Actinobacteria. Our results suggest that changes in inundation frequency in floodplain wetlands may alter the subtle balance of microbial communities, affecting wetland soil health and microbial diversity in those environments.