This dataset contains stable isotope (δ13C) and radioisotope (Δ14C) compositions of dissolved inorganic carbon, dissolved organic carbon, particulate organic carbon, and bed material organic carbon samples collected from rivers in the Upper Mississippi River Basin between October 2014 and February 2016. Rivers were sampled at USGS gaging stations: Minnesota River at Fort Snelling State Park, MN (gage #05330920), Mississippi River at Hwy 610 in Brooklyn Park, MN (gage #05288500), St. Croix River at Prescott, WI (gage #05344490), Mississippi River at Prescott, WI (gage #05344500), and Chippewa River at Durand, WI (gage #05369500). One site was also sampled at a location that is not co-located with a gaging station: Mississippi River at Wabasha (44.38772, -92.03616). Each site was sampled approximately every 3 months.