We conducted a study to investigate the characteristics of the carbon cycle of two streams (located in Shiga Prefecture, Japan), having similar size, namely, the Adokawa stream (length: 52 km, area: 305 km2, watershed population: 8,000) and the Yasukawa stream (length: 62 km, area: 380 km2, watershed population: 120,000), but with different degree of human activity. Samples were collected from these two streams at 14 (Adokawa stream) and 23 (Yasukawa stream) stations in the flowing direction. The dissolved inorganic carbon (DIC) concentration and the stable carbon isotope ratio of DIC (δ13C-DIC) were measured in addition to the watershed features and the chemical variables of the stream water. The δ13C-DIC (-9.50 ± 2.54‰), DIC concentration (249 ± 76 μM), and electric conductivity (52 ±13 μS/cm) in Adokawa stream showed small variations from upstream to downstream. However, the δ13C-DIC (-8.68 ± 2.3‰) upstream of Yasukawa stream was similar to that of Adokawa stream and decreased downstream (-12.13 ± 0.43‰). DIC concentration (upstream: 272 ± 89 μM, downstream: 690 ± 37 μM) and electric conductivity (upstream: 69 ± 17 μS/cm, downstream: 193 ± 37 μS/cm) were higher downstream than upstream of Yasukawa stream. The DIC concentration of Yasukawa stream was significantly correlated with watershed environmental variables, such as, watershed population density (r = 0.8581, p<0.0001, n = 23), and forest area percentage of the watershed (r = -0.9188, p<0.0001, n = 23). δ13C-DIC showed significant negative correlation with the DIC concentration (r = -0.7734, p<0.0001, n = 23), electric conductivity (r = -0.5396, p = 0.0079, n = 23), and watershed population density (r = -0.6836, p = 0.0003, n = 23). Our approach using a stable carbon isotope ratio suggests that DIC concentration and δ13C-DIC could be used as indicators for monitoring the health of stream ecosystems with different watershed characteristics.