Time series of stable isotopes (δ2H and δ18O) were analyzed in water samples collected near the A. P. Møller Skolen, Schleswig (Kleine Breite, Schlei), in biweekly to monthly intervals between March 2020 and March 2021. Water was sampled with a pipette from ca. 0.5 m below water surface and directly transferred into a measurement vial. 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 modular WTW 3440 multiparameter devices and regularly calibrated conductivity cells (MPP 930 IDS, TetraCon® 925-P). The data give information about the seasonal isotope amplitude at the sampled locations and about spatial variability along the transects.