The aquarium at the Besançon Museum is located in the heart of the Vauban Citadel, perched above the city. It houses aquatic fauna from the rivers of Franche-Comté and its wetlands. Integrated within a vaulted room of the Arsenal, it shelters around one hundred species of fish, amphibians, and freshwater invertebrates.

Since 2005, the aquarium has been involved in unique conservation programs to preserve iconic species such as the Rhône Apron and native crayfish. These efforts to safeguard aquatic wildlife have yielded a wealth of new knowledge about these little-known species and have generated thousands of specimens through captive breeding. These species have then been reintroduced into the wild to support existing populations.