Anthropogenically-driven climate change will very likely alter marine ecosystems in the future. Unique environments (i.e., volcanic CO2 seeps and semi-enclosed bays) that act as natural analogues of future oceans are valuable resources for studying the effects of climate change on marine ecosystems. Our study examined fish assemblages at the semi-enclosed bay of Bouraké, New Caledonia, where coral reefs are subjected to multiple environmental stressors such as temperatures, pH, and dissolved oxygen close to, or even worse than projected conditions under future climate change. By utilizing environmental DNA (eDNA) metabarcoding and underwater visual surveys (UVC), we detected a shift in fish assemblages between the natural analogue of Bouraké and a nearby control reef.We detected eight species from the Acanthuridae, Chaetodontidae, and Pomacentridae families, which seem to be utilizing the Bouraké, suggesting that some species can take advantage of the environmentally driven shifts in habitat due to extreme environmental conditions in Bouraké. Additionally, some species of Labridae and Scaridae were absent from Bouraké and may be less tolerant to extreme conditions. The combination of eDNA and UVC surveys highlights the strength of combining both methods to characterize the fish assemblage and the importance of natural analogues in expanding our understanding of the ecosystem-level responses of fishes to future ocean conditions.