Due to the complex hydrogeological conditions in karst regions, it is difficult to measure sediment source contributions at a catchment scale directly. The objective of this study was to quantify the relative contributions of sediment sources and their temporal variability in a karst catchment in southwest China. Karst depressions can trap eroded sediment similar to a dam or reservoir and, thus, are representative and typical test beds for identifying sediment sources in karst regions. Three sediment cores were taken from a karst depression, 58 soil samples from three potential sediment sources were collected, and 18 soil properties were analyzed. The relative contributions of cropland, forestland, and fissure or crack soils were calculated using a multivariate mixing model. The fingerprinting results demonstrated that the cropland was the main sediment source in karst catchment. Specifically, according to the mean sediment contributions of the three deposited sediment cores, the sediment contribution from cropland topsoil was 69.3%, varying from 46.9% to 92.3%, and forestland soil and crack soil accounted for 8.6% and 22.1% of the sediment yield, and varying from 2.8% to 16.5% and 4.8%–36.6%, respectively. This result indicated that great attention should be paid when using only a single core to quantify sediment provenance. Due to the deposited sediment was generally disturbed as cropland in the karst depression, the area that has not been disturbed in recent decades in depression was more appropriate to trace sediment sources in karst catchment. To the best of our knowledge, this study was the first to quantify the contributions of sediment sources in the karst catchment of southwest China. This study provides valuable information and a preliminary reference for applying a composite fingerprinting technique to quantify sediment sources in karst catchments.