Our dataset contain brachiopod and bulk carbonate rock stable isotopic data for oxygen (O) and carbon (C) from the Middle Ordovician succession from northern Estonia region for evaluating the Middle Ordovician palaeotemperature and palaeoenvironmental history. Combining the published and new δ13Cbrac and δ18Obrac data allow us to address chemostratigraphic correlation in the interval Middle Ordovician. The Baltoscandian δ18O data generally confirm a cooling trend from Early to Middle Ordovician documented by previous studies in different palaeobasins. A total of 50 brachiopod and 30 bulk rock samples were collected for this study from eight outcrops in northeastern Estonia.