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The sedimentary record of the Caspian Basin is an exceptional archive for the palaeoenvironmental, palaeoclimatic and biodiversity changes of continental Eurasia. During the Pliocene-Pleistocene, the Caspian Basin was mostly isolated but experienced large lake level fluctuations and short episodes of connection with the open ocean as well as the Black Sea Basin. A series of turnover events shaped a faunal record that forms the backbone of the Caspian geological time scale. The precise ages of these events are still highly debated, mostly due to the lack of well-dated sections. Here, we provide an integrated magneto-biostratigraphic age model for two sections from the Kura Basin – Goychay and Hajigabul. Our results reveal several major intervals with elevated salinity, associated with mesohaline faunas, and propose the following age constraints: 1) The Productive Series-Akchagylian boundary is marked by a marine transgression from the open ocean that occurred around the Gauss-Matuyama reversal (∼2.7–2.6 Ma); 2) The Akchagylian-Apsheronian transition is characterized by a regression event and introduction of a new, “Pontocaspian” mollusc assemblage, dated within the Reunion subchron (∼2.13 Ma). The ostracod assemblages of the two sections do not show a major faunal turnover here; 3) The early Bakunian transgression occurs after the upper Apsheronian lowstand (0.85–0.83 Ma). We conclude that major transitions in the age-indicative mollusc groups sometimes occur at different time intervals (i.e. diachronic) and are highly depended on the local depositional environments. A high-resolution interdisciplinary approach on sections outside the Kura Basin is required to better understand the potential diachroneity of these turnover events in the entire Caspian Basin.