[Objective] Carbon storage dynamics and its driving mechanism were explored aims to provide scientific basis and methodological reference for regional sustainable development as well as soil and water resource conservation. [Methods] Taking Taohe River basin in the Tibetan Plateau and Zuli River basin in the Loess Plateau as study areas, the direct and indirect effects of climate, vegetation, water and sediment on net primary productivity (NPP) were investigated. The influence threshold of different factors on NPP was quantified by means of elastic coefficient and density analysis. [Results] ① The mean NPP values (calculated by carbon) in the Taohe River and Zuli River basins were 276.47 and 136.86 g/m², respectively, with significant spatial variations. ② In the Taohe River basin, NPP was predominantly influenced by moisture parameters (P), followed by the normalized vegetation index (NDVI). In contrast, temperature (T) and soil erosion (A) had negative but relatively minor effects. In the Zuli River basin, NPP was primarily affected by NDVI and water retention (W_R), while T and A exhibited similar negative effects, though with a greater absolute value compared to the Taohe River basin. Spatially, the strongest explanatory power for NPP distribution was observed when T and NDVI interacted in both watersheds. ③ The threshold quantification results varied across methods. In the Taohe River basin, the thresholds for T and A effects on NPP were reached earlier, whereas in the Zuli River basin, the thresholds for P, NDVI, and W_R effects on NPP were attained first. [Conclusion] The dynamics of carbon storage exhibit distinct driving forces and their affecting threshold variations under different ecological and geographical conditions. Before the affecting values reach the “sustainable” threshold, excessive human intervention is unnecessary, but mainly carrying out some works related to climate monitoring. Once the affecting values reach the “restrictive” threshold, measures for rational water resources allocation, soil erosion control, and mitigation of river sediment transport should be taken promptly.