Climate change is warming estuaries globally. Eastern Australian estuaries are warming faster than predicted for Earth’s oceans, at a rate of 0.2 °C year-1. While Vibrios are ubiquitous in estuarine microbiomes, several species are pathogenic to humans and marine organisms. The warming of temperate waters has increased Vibrio abundance and disease in these systems, with Vibrio species subsequently recognised as a barometer of climate change. We sampled Lake Macquarie, a temperate east Australian estuary, subject to thermal pollution from power stations with receiving bays an average 6°C warmer than ambient lake temperature. We assessed prokaryote community composition using 16S rDNA metabarcoding as well as Vibrio-specific quantitative PCR and amplicon sequencing of hsp60 genes to quantify total Vibrio gene copies and identify Vibrio species in an estuarine fish and surrounding seawater. At the warmest site, total Vibrio gene copies were elevated in fish hindguts, and potential pathogenic Vibrio species were identified. The fish gut microbiota at this site also displayed evidence of dysbiosis, with decreased species richness and beta diversity and proliferation of a potentially pathogenic Vibrionaceae. These data indicate that warming is likely to result in increased abundances of potentially pathogenic Vibrio species in temperate estuarine systems.