Karst depression is a common landform type in karst areas of Chongqing. Small depression watershed is an important place for agricultural activities. Studying the characteristics of erosion and sediment yield of different land uses in the watershed is of great significance for understanding the laws of erosion and sediment production and controlling soil and water loss. A small karst depression basin with a reservoir was selected, and 39 geochemical properties of the sediment source as well as sediment samples were analyzed. The composite fingerprint and multivariate mixed model were used to calculate the erosion and sediment contribution rate of each sediment source. The results showed that the best fingerprint factor combination screened by the catchment was U, χ_lf, Rb, Li, ¹³⁷Cs, χ and Mn. The cumulative rate of correct discrimination was 99.93%, and the total correct discrimination rate of the six sediment sources was 91.49%, which accorded to the application conditions of compound fingerprint method. The relative contributions to sediments in the basin of carbonate arable land, carbonate woodland, carbonate grassland, clastic rock forest, clastic grassland and trench/fissure soil were 16.29%, 41.16%, 13.03%, 16.67%, 4.48% and 8.37%, respectively, the goodness of fit of the model was 93.57%, and the average relative error was 8.26%, indicating that the model result was credible. Among all sediment source areas, the sediment contribution per unit area of carbonate rock farmland was far higher than that of other sediment source areas, which was 1.98 times that of carbonate forest land, 2.07 times that of carbonate grassland, 2.13 times that of clastic rock forest land, and 2.21 times that of clastic rock grassland. The soil corrosion resistance of carbonate rock farmland per unit area was the weakest.