Net CO2 flux (FC) time-series and the respective random error (RE) estimations at 30 min time step of the period 2018 - 2020 from two urban eddy covariance sites in the center of Basel. Data are produced using the EddyPro® Software v7.0.6 (LI-COR Inc.). The main processing steps include axis rotation for tilt correction using the double rotation method, linear detrending to extract turbulent fluctuations, covariance maximization for time-lag compensation between the gas analyser and the sonic anemometer and density fluctuation compensation. Spectral corrections are also applied to flux estimates for low and high frequency losses. Quality flagging is performed according to steady state and integral turbulence characteristics tests based on the 3-point flagging system of Mauder and Foken. Flux random uncertainty estimation is performed according to the method of Finkelstein and Sims (2001). The time-series are filtered according to multiple criteria to avoid problematic values. Data format: comma separated values (csv) Time step: 30 min Station acronym Geographic location Sensor height (m a.g.l.) Sensor models (sonic anemometer, gas analyser) Sonic azimuth (o) Acquisition frequency (Hz) BKLI 47.56173 °N, 7.58049 °E 39 HS-100 (Gill Instruments Ltd.), LI-7500 (LI-COR Inc.) 0 20 BAES 47.55123 °N, 7.59560 °E 41 CSAT3 (Campbell Scientific Inc.), LI-7500 (LI-COR Inc.) 340 20