These data were collected by the University of Montana and Montana State University to support the Upper Clark Fork River restoration monitoring project supported by the US NSF Long Term Research in Environmental Biology (LTREB) program. The original analytical intent for these data was to assess the response of river metabolic regime to the floodplain restoration via inference of whole-ecosystem metabolism from the daily variation in carbon dioxide concentrations. Data are primarily measurements of dissolved carbon dioxide, pH, electrical conductivity, and temperature in well-mixed river thalweg water. Additional miscellaneous data were collected for quality control. Data are from late in the 2017 field season. Data were collected on the Upper Clark Fork River (USGS HUC 17010201) at the Galen and Racetrack sites northeast of Anaconda, Montana, USA. High frequency carbon dioxide and pH data were collected using field deployments SAMI sensors from Sunburst Sensors (Missoula, Montana, USA). Electrical conductivity data was collected with a HOBO sensor from Onset Computer Corporation (Bourne, Massachusetts, USA).