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Aquatic biodiversity in Alabama ranks very high nationally, due in part to the state’s numerous river systems and diverse geology. Biological field monitoring of the state's abundant aquatic faunas is used as a tool to assess the water quality in the state. This information collected by the Geological Survey’s Ecosystems Investigations Program (EIP) is used in resource management and species distribution studies and is available for public use. The Program also maintains small reference collections of fishes, mussels, crayfishes, and aquatic insects that are available for scientific use or public tour.

Investigations by EIP biologists have documented the habitats and distributions of fishes all over the state. Biological/water-quality monitoring studies have assessed the impacts of pollution, timber management practices, coalbed methane production, and coal mining on aquatic ecosystems in watersheds throughout Alabama. Surveys of Alabama’s rich mussel fauna (include a link to mussel open file reports here) are being performed in numerous river systems, and EIP group is also assisting in monitoring the relatively unknown crayfish fauna of the state.