Stable isotopes (δ2H and δ18O) were analyzed in water samples collected at 68 spots along the Schlei, the Zingster Bodden chain, and the Rügener and Greifswalder Boddens in June 2019, March 2020, and July 2021. Transect samples were taken at shores from 0.3 to 0.6 m below water surface, using a pipette, and directly transferred into measurement vials. Isotope analysis was conducted at IGB Berlin, using a Picarro L2130-i cavity ring-down spectrometer. Water chemical parameters were measured in-situ with a WTW multiparameter device (Multi 3630 IDS), equipped with a WTW TetraCon 925 electrical conductivity measuring cell. The data give information about the spatial isotope variability along the transects.