Microscale microbial distributions are patchy, with abundance hotspots and cold - spots that provide important microenvironments for microbial interactions. However, studies are often restricted to abundance estimates alone. At the riverbed of the Murray River, we used taxonomy to complement quantitative analysis to show that abundance hotspots, coldspots and background levels are taxonomically distinct at all taxonomic levels. Abundance hotspots varied 115- and 5.9-fold above background over 0.9 cm for viruses and bacteria, respectively. For bacteria, hotspots represent increases in particular taxa rather than in all bacteria. Genera with increased abundances-Pseudomonas, Parasporobacterium, Lachnospiraceae incertae sedis and Bactero ides - were indicative of human and animal inputs, and represented up to 14.7% of the community. Distinct dominant genera led to high taxonomic dissimilarity among hotspots. Genera exclusivity was still higher in the background and coldspots, with 54 and 48 exclusive genera compared to 7 and 4 genera in hotspots, suggesting hotspots from persistent genera, rather than introduced genera. Hotspots were more similar to coldspots than background, suggesting coldspots may represent dying hotspots. Sample category predicted taxonomic similarity better than proximity, further indicating these heterogeneities are distinct from the background at the sub-centimetre scale. Hotspots and coldspots represent distinct spatial taxonomic distributions, rather than changes of the overall community. This suggests 0.3 ml volumes are cohesive long enough for particular operational taxonomic units (OTUs) to increase and create taxonomically distinct microscale communities within the Kolmogorov and Batchelor scales.