This dataset includes raw and processed data, as well as modeling codes that were used to produce the results presented in Schulz et al. (submitted) "Moving bedforms control CO2 production and distribution in sandy river sediments" submitted to Journal of Geophysical Research: Biogeosciences. The dataset contains: 1) Data for sediment characterization: Grain size distribution, hydraulic conductivity, loss on ignition, and porosity data. 2) Data on hydrology and morphodynamics: Bedform celerity, height, and length, Damkoehler number, shear velocities, and Python codes for modeling the hyporheic exchange flux. 3) Data compilation: Data of online sensors that continuously measured various parameters of the streamwater, atmospheric pressure, and CO2 air concentrations. 4) Digital raw images of dye tracer experiments. 5-10) Image data: Raw and processed planar optode and IR images, spreadsheets containing data analysis results.

This research was funded by the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 765553 (EuroFlow) and the Israel Science Foundation, grant 682/17. Further funding was supplied by the German Research Foundation (DFG) as part of the research project "Urban Water Interfaces (UWI)" (GRK 2032), and by the German Federal Ministry of Education and Research (BMBF) and the Israeli Ministry of Science, Technology and Space (MOST) in the framework of the German-Israeli Cooperation in Water Technology Research as part of the Young Scientist Exchange Program (YSEP136).