Water isotopes (δ²H and δ¹⁸O) were analyzed in samples from lakes and rivers in eastern Germany. This sub-dataset is derived from water samples collected from lake and river shores. Seasonal samples were collected in March, July, October 2022, and in March 2023, with a plastic syringe from 20-50 cm depth below water surface and directly filtered and transferred into a measurement vial. Stable isotope analysis was conducted at IGB Berlin, using a Picarro L2130-i cavity ring-down spectrometer. Measurement uncertainty was quantified to <0.5 ‰ for δ²H and <0.2 ‰ for δ¹⁸O. Water chemical parameters were determined in-situ with a portable WTW-multiparameter probe. The data give information about the seasonal isotope amplitude at the sampled spots and about spatial isotope variability in different branches of the associated river systems.