This dataset presents measurements of stable isotopes in biogenic carbonates (δ13C and δ18O) from Lake Locknesjön, Sweden. Carbonate samples were collected in 2018 from different lacustrine organisms along a water depth gradient from 0 to 8 m depth: encrustations from the calcifying algae Chara hispida, valves from the bivalve mollusk Pisidium sp., and valves from two species of ostracods, Candona candida and Candona neglecta. Adult specimen and different juvenile stages of the ostracods were sampled. The carbonate samples originate from living organisms, i.e. which were alive at the time of sampling in 2018, and from their subfossil remains in the uppermost centimeter of the lake sediments. The carbonate samples were collected by a diving team. Carbonate isotope measurements were carried out at MARUM, Bremen, Germany, using a ThermoFisher Scientific 253plusgas isotope ratio mass spectrometer with a Kiel IV automated carbonate preparation device. The standard deviation of the reference standards over the measurement period was 0.06‰ for δ18O and 0.03‰ for δ13C.