The Caspian Sea is an evolutionary island whose rich and endemic fauna have evolved in partial isolation over the past two million years. Baseline studies of pre-20^th Century communities are needed in order to assess the severity of the current Caspian biodiversity crisis, which mostly involves invasive species. An inventory of late Holocene shelly assemblages (c. 2000–2500 cal yr BP) from outcrops in and around Great Turali Lake (Dagestan, Russia) shows a diverse nearshore community consisting of 24 endemic Caspian species, two invasive species and two Caspian native species that lived in a shallow embayment with mesohaline salinities of circa 5–13 psu (parts per thousands). This pre-crisis Holocene Caspian mollusc community serves as a baseline against which modern mollusc diversity measurements can be evaluated. Examination of faunas from similar environments living today and in the past illustrates the dramatic changes in nearshore communities during the 20^th Century. Our study identifies a habitat that may have served as a refuge, but that is currently under threat from invasive species. The severity of the Caspian biodiversity crisis is comparable with other well-known biodiversity crises in semi-isolated ecosystems such as the cichlid fish communities of Lake Victoria, Africa.