Water isotopes (δ2H and δ18O) were analyzed in samples collected in lakes associated to major riverine systems in northeastern Germany throughout 2020. This sub-dataset is derived from water samples taken before the outflow of Müggelsee. Sampling was conducted biweekly from March 2020 to January 2021. Samples were taken with a pipette from 40-60 cm 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 and physical parameters are daily average values derived from the Müggelsee long-term data monitoring station (https://emon.igb-berlin.de/grosser_mueggelsee.html). The data give information about the seasonal isotope amplitude at Müggelsee over the studied time period.