<p>Water isotopes (δ<sup>2</sup>H and δ<sup>18</sup>O) were analyzed in samples collected in lakes associated to riverine systems in northeastern Germany throughout 2020. The dataset (Aichner et al., 2021) is derived from water samples collected at a) lake shores (sampled in March and July 2020); b) buoys which were temporarily installed in deep parts of the lake (sampled monthly from March to October 2020); c) multiple spatially distributed spots in four selected lakes (sampled in September 2020); d) the outflow of Müggelsee (sampled biweekly from March 2020 to January 2021). At shores, water was sampled with a pipette from 40–60 cm below water surface and directly transferred into a measurement vial, while at deeper parts of the lake a Limnos water sampler was used to obtain samples from 1 m below surface. Isotope analysis was conducted at IGB Berlin, using a Picarro L2130-i cavity ring-down spectrometer. The data give information about the seasonal isotope amplitude in the sampled lakes and about spatial isotope patterns in different branches of the associated riverine systems.</p>