Autochthonous dissolved organic matter (Auto-DOM) produced by a biological carbon pump using dissolved inorganic carbon (DIC) from carbonate weathering plays an important role in carbon cycling within inland waters. However, little is known regarding how environmental conditions impact the composition and fate of organic matter, especially in surface waters of the semi-arid Loess Plateau, which is enriched in DIC by significant carbonate weathering. To obtain novel insight, we combined hydrochemistry, isotopic composition (δ²H, δ¹⁸O, and δ¹³C_DIC), Rayleigh fractionation model, optical spectroscopy (absorbance and fluorescence), and Fourier transform ion cyclotron resonance mass spectrometry measurements to elucidate how primary production and hydrology impact the composition of DOM and the stability of the resulting Auto-DOM throughout the river–reservoir–wetland aquatic continuum of the Bahe River in the carbonate-mineral-rich semi-arid Loess Plateau where carbonate weathering is significant. The Rayleigh fractionation model results indicated that watershed DIC is primarily consumed through aquatic primary production rather than CO₂ degassing. Further investigation revealed that primary production and evaporation co-occurred in this watershed. With the enrichment of the stable water isotope δ²H, the relative abundances of the allochthonous compounds decreased and the relative abundances of the autochthonous substances increased, suggesting that the terrestrial signal of riverine DOM decreased while autochthonous production increased along the flow pathway. In addition, associations between optical and molecular characteristics among DOM samples from different water bodies revealed that the stability ratio (Fmax(C2/(C2 + C4))) of Auto-DOM to the ratio of carboxylic-rich alicyclic molecules showed a consistent trend, suggesting that phytoplankton-derived and biomineralized C2 compounds are potentially recalcitrant DOM in inland waters. We conclude that hydrology and primary production affect the source, composition, and, potentially, the stability of DOM in DIC-enriched surface waters of the semi-arid Loess Plateau, which may lead to a more humic-like DOM composition in inland water and export this lower bioavailability DOC to the ocean in the long term.