Stable isotopes (δ²H and δ¹⁸O) were analyzed in water samples collected at the German Baltic Sea Coast. Transect samples were taken in June 2019, March 2020, and July 2021 at 68 spots along the Schlei, the Zingster Bodden chain, and the Rügener and Greifswalder Boddens. Additionally, at selected spots time series were sampled in biweekly to monthly intervals between March 2020 and March 2021. At shores, water was sampled with a pipette from 0.3 to 0.6 m below water surface and directly transferred into a measurement vial. In deeper parts of the boddens a Limnos sampler was used to obtain water from 0.5 to 1 m below surface. Isotope analysis was conducted at IGB Berlin, using a Picarro L2130-i cavity ring-down spectrometer. The measurement uncertainty was quantified by error propagation, including the parameters a) uncertainties of lab standards; b) errors of standard calibration; c) average standard deviation of replicate measurements. Based on this, measurement uncertainty was estimated to account 0.16 ‰ for δ¹⁸O and 0.57 ‰ for δ²H. Water chemical parameters were measured with WTW measurement devices. The data give information about a) the seasonal isotope amplitude at the sampled locations; b) spatial variability along the transects, and c) the correlation between isotopes and water chemical parameters.