Carbon plays an important role in global climate change. The mechanisms of carbon sources and carbon sinks have also received wide attention from society, and the physical and chemical characteristics of riverine ions can reflect the chemical weathering of rocks and carbon sink capacity of river basins. Based on the data on river, rainwater, and rock samples from 2019, this study used various methods, such as ion ratio diagrams and ternary diagrams, to analyze the chemical characteristics of water; the chemical weathering and carbon sink effects of rocks were also calculated while assuming three scenarios based on the main sources of ions in the Naqu River. The results showed that for the whole catchment, the main ion sources in the river were: carbonate rock chemical weathering > silicate rock chemical weathering > evaporite dissolution > atmospheric precipitation input. According to the calculations, in the three scenarios, the carbonate weathering rates were 16.84, 11.32, and 14.08 t/km2/yr, and the carbon sink capacities were 66.47, 121.13, and 93.80 mol/km2/yr, respectively; the evaporite weathering rates were 2.20, 9.63, and 5.92 t/km2/yr, respectively. The silicate chemical weathering rate and carbon sink capacity did not change significantly in either scenario, with 6.82 t/km2/yr and 248.6 mol/km2/yr, respectively. This study quantified the ion sources in the Naqu River basin and accurately analyzed their chemical genesis, which helps in understanding the role of the rivers of the Qinghai–Tibet Plateau in the global carbon cycle and global climate change, in addition to providing a reference for the scientific development of the Nujing River.