This dataset supports the publication "Dry-to-flow mode: impacts on river carbon and nitrogen dynamics". In where we investigated how instant and gradual surface flow resumption (the latter preceded by 6 h inundation), combined with six flow velocities and five levels of sediment transport, affect streambed biogeochemistry in the Queich River (Germany). Over 24 h, we measured CO₂, CH₄, and N₂O fluxes, porewater gas concentrations, and dissolved oxygen dynamics. Additionally, we applied a ¹⁵N-NO₃ tracer to track denitrification via changes in δ¹⁵N-N₂, and determined NO₃⁻ and NH₄⁺ release and uptake rates. The repository also includes videos documenting sediment transport conditions at flow velocities of 0.15, 0.17, 0.18, and 0.21 m s⁻¹.