In the Russian Federation, the protection category “Zapovednik” represents a strictly protected area, where the access is restricted and the aim is to keep the area “forever wild”. We provide an overview about the organization of these nature reserves and highlight their contribution to fundamental research. Aquatic ecosystems in zapovedniks provide pristine sites of great importance for long-term monitoring and research, which fosters process understanding regarding interannual variability and development of aquatic coenosis. We present a long term monitoring and research project about abiotic and biotic parameters in the Central Forest State Nature Biosphere Reserve. Examples from the Privolzhskaya Lesostep Nature Reserve include monitoring of invasive fish as well as analyses about the influence of beavers on fish. The Astrakhan Biosphere Nature Reserve in the Volga delta is a hotspot for fish biodiversity; thus, there the state nature reserve security service plays an important role to avoid poaching. Our case studies from the Volga Basin exemplify the structure and function of nature reserves and highlight their contribution to research, protection and management of aquatic ecosystems. Long-term datasets from the zapovedniks can (i) improve process understanding, (ii) ensure protection of aquatic systems and sustainable water management and (iii) support knowledge-based decisions.