Water isotopes (δ²H and δ¹⁸O) were analyzed in samples from a range of relatively small lakes and ponds in northeastern Germany. The sampled water bodies are not connected to major river systems but are either fed by groundwater or small creeks. Water chemical parameters were determined in-situ with a portable WTW-multiparameter probe. Water samples were collected in different seasons of the years 2020, 2022 and 2023. Here, composite samples were taken from the lake centers with a Ruttner Water Sampler in 2 m intervals from the lake surface to bottom. In some cases, only a surface sample was collected from 50 cm depth using a pipette. Samples were 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. The data give information about the seasonal and spatial stable isotope variability at the sampled lacustrine systems.