Radiocarbon natural abundances (Δ14C) are being increasingly used to trace carbon cycling in stream ecosystems. To understand the ultimate sources of carbon, we determined the stable carbon isotope ratios (δ13C) and Δ14C values of dissolved inorganic and organic carbon (DIC and DOC, respectively) and of particulate organic carbon (POC) in two small streams in central Japan, one of which flows over limestone bedrock (Seri) and the other does not (Fudoji). Investigations over four seasons revealed that the Δ14C values of the DIC (from −238‰ to −174‰ for Seri and −23‰ to +10‰ for Fudoji) were less variable than those of the other carbon fractions (DOC: from −400‰ to −138‰ for Seri and −2‰ to +103‰ for Fudoji; POC: from −164‰ to −60‰ for Seri and −55‰ to +37‰ for Fudoji). Based on mass balance calculations using the δ13C and Δ14C values, the proportions of carbon in the DIC originated from (1) atmospheric CO2 were 47% to 57% for Seri and 74% to 90% for Fudoji, (2) organic matter degradation were 29% to 35% for Seri and 4% to 21% for Fudoji, and (3) carbonate rock were 14% to 22% for Seri and 4% to 6% for Fudoji. We compared the results with previous studies that had been conducted in larger rivers and showed that in small streams, the dissolution of atmospheric CO2 and weathering of carbonate rock are more important factors in the carbon cycling than the biological degradation of organic matter.