This dataset contains concentrations of dissolved organic carbon, inorganic carbon, CO2, CH4 and N2O in the Black Burn stream which drains Auchencorth Moss peatland in South East Scotland. Concentrations and fluxes have been measured within the Black Burn on an approximately weekly to fortnightly basis from approximately 2006 to present (see https://doi.org/10.5285/3f0820a7-a8c8-4dd7-a058-8db79ba9c7fe ). Concentrations in this dataset are from a series of new sites, upstream of the long-term sampling record, adjacent to an area of drains blocked by Scottish Natural Heritage. Measurements began during the drain blocking. Data was collected initially as part of a masters project for University of Edinburgh through Scotland's Rural College and continued by the Centre for Ecology & Hydrology. Full details about this dataset can be found at https://doi.org/10.5285/88ffbf44-0ec0-41d6-9814-04bc3535cd84