These data were collected to study oxidative weathering processes in the Waiapu River catchment, New Zealand, with potential carbon release sourced from the oxidation of petrogenic organic carbon or carbonate dissolution coupled to the oxidation of sulfide minerals. There, in mudstones exposed in a highly erosive gully complex, in situ CO2 emissions were measured with drilled gas accumulation chambers following the design by Soulet et al. (2018, Biogeosciences 15, 4087-4102, https://doi.org/10.5194/bg-15-4087-2018 ). Temporal and spatial variability in CO2 flux can be put in context with environmental changes (e.g., temperature and hydrology). For this, CO2 release from 5 different chambers, which were installed over a transect of ~ 10 m length in a gully above a nearby streambed, was measured several times over a short study period (circa one week). In addition, the gaseous CO2 storage (partial pressure) in the shallow weathering zone was measured prior to a CO2 flux measurement. To understand the source of CO2, gas samples were collected and their stable and radioactive carbon isotope compositions determined. In this process, we identified a contaminant, which was associated with the chamber installation, that can be traced in the gas samples that were collected within 4 days following the installation. Details of the subsequent data analysis and interpretation can be found in: Roylands et al. 2022, Chemical Geology: Capturing the short-term variability of carbon dioxide emissions from sedimentary rock weathering in a remote mountainous catchment, New Zealand. This work was supported by the European Research Council (Starting Grant to Robert G. Hilton, ROC-CO2 project, grant 678779).