Measuring community changes in response to perturbations is a fundamental aspect of ecological study. Molecular biology has provided ecologists with a suite of techniques that enhance our capacity to detect a wide range of organisms, particularly microscopic organisms or those difficult to study or identify. Given the relative infancy of ecogenomics, there are a limited number of studies that demonstrate some of the wider benefits of a genomic approach to study community changes. We applied an ecogenomic approach where we measured whole eukaryote community structure (animals, plants, fungi) in two Murray River studies. In the first instance we could show strong differences in the community present on biofilms and water column samples, at two contrasting sites. In the second study we tracked the community structure of riverine biofilms during and after exposure to a flooding event. While there were times when clear differences could be seen between sites, no clear picture emerged in response to the flood waters. Further work is required to determine whether there was indeed no consistent change in response to the flood, or whether methodological issues obscured any real response.