Abstract: The stability of karst carbon sink is the research fronts in Earth Sciences. Rivers are the key sites for the migration and transformation of karst carbon sink, where the sediment acts as an important component of the aquatic carbon pool and accumulates a large amount of organic carbon. Therefore, uncovering the physicochemical properties of river sediments is crucial to understand the carbon cycle in karst aquatic ecosystem. Here, we took the Zhaidi River which fed by the Haiyang-Zhaidi underground river system as the object, the physicochemical properties and sources of organic carbon were analyzed through the field surveys and indoor chemical analysis. Our aim was to elaborate the influence of karst aquatic environment and submerged macrophytes on the sediments. The results showed that: (1) The spatial heterogeneity of sediments was remarkable, and the sediments were mainly composed of 0.075—2 mm sandy particles with pH ranging from 8.23 to 8.88, TOC of 1.2—9.5 g/kg, TN of 289—1241 mg/kg, TP of 497—743 mg/kg, \rmNH^+_4 -N of 7.14—17.10 mg/kg, \rmNO^-_3 -N of 3.06—7.00 mg/kg, and C/N of 4.15—12.47. The pH of the sediment was positively correlated with particle size and negatively correlated with TOC, TN and NH⁺₄-N, and TOC was significantly positively correlated with TN, indicating that the sources of carbon and nitrogen in sediments were consistent. (2) Situated in the alkaline karst water environment, the sediment showed the alkalinity as well, and the higher the sediment pH, the larger the particle size. In addition, the change of the grain size affected the contents and distribution of N and P in the sediments. (3) In the sediments, the TOC mainly originated from the inorganic carbon captured by the photosynthesis of submerged macrophytes, and its biomass influenced the physicochemical properties of the sediments, especially the C/N. In sum, in the karst spring-fed river, submerged macrophytes transformed the unstable inorganic carbon which originated from the karstification into stable organic carbon, and stored it into the sediment carbon pool. These processes significantly enhanced the stability of karst carbon sink.