This study provides 87Sr/86Sr, δ13C and δ18O data from the best-preserved limestone and dolomite of the Ediacaran carbonate-dominated Khorbusuonka Group of the Olenek Uplift, NE Siberian Craton, as well as detrital zircon geochronological data from both underlying and overlying sandstones. The Maastakh Formation is characterized by 87Sr/86Sr ratios of ca. 0.70822 and δ13C values between + 4.8 and + 6.0‰. 87Sr/86Sr ratios in limestones of the Khatyspyt Formation are fairly uniform, ranging from 0.70783 to 0.70806. The carbon isotopic composition slowly decreases from bottom (+ 3.7‰) to top (− 0.2‰) of section. The Sr isotopic composition of the Turkut Formation varies from 0.70824 to 0.70914, value of δ13C is about zero: − 0.7…+0.7 ‰. The youngest population of detrital zircons from Maastakh Formation indicates that these rocks were formed not later than 630 Ma. U–Pb detrital zircons data of Kessyusa Group has a single peak at about 543 Ma, which is almost identical to the earlier dating. Based on biostratigraphy and isotopic data, the Sr isotopic compositions from the Khatyspyt Formation (87Sr/86Sr = 0.70783–0.70806) represent the composition of seawater at 560–550 Ma. Such low values of 87Sr/86Sr ratio in Ediacaran water were probably caused by the quick opening of Iapetus Ocean.