Intensive agricultural activities have accelerated soil erosion and rocky desertification in karst regions of southwest China. Knowledge of sediment sources and soil erosion rates can be used to target soil conservation measures and to improve calibration and validation of process-based soil erosion and sediment delivery models for scenario analyses. Due to the complexity of karst environments, however, catchment scale information on these components of sediment budgets has rarely been assembled, meaning there continues to be an evidence gap. Within this context, this study selected Chenqi catchment, given its appropriate research infrastructure, to investigate sediment sources and soil loss rates in a typical karst agroforestry landscape. We estimated the relative contributions from three sources: surface soil, subsurface soil and clastic rock, using a composite fingerprinting procedure combining Cs-137 and magnetic susceptibility and a frequentist un-mixing model with Monte Carlo uncertainty analysis. Suspended sediment samples were taken at an hourly interval during seven rainfall events in 2017-2018 to characterize and quantify the sediment exported in both surface and underground drainage. The overall average median contributions (with 5th-95th percentile uncertainty ranges) from the sources to the suspended sediment samples from the surface drainage outlet were in the order: 62% (0-99%) subsurface soils, 25% (0-91%) surface soils and 13% (0-45%) clastic rock. For the sediment samples collected from the underground drainage catchment outlet, the corresponding estimates were in the order: 68% (0-97%) subsurface soils, 25% (0-53%) clastic rock and 7% (0-44%) surface soils. Plot scale soil loss rates were highest on cropland (0.70 Mg km(-2)) and pasture land (0.48 Mg km(-2)). The average (2017 and 2018) annual suspended sediment load exported through the surface outlet was 4.64 Mg km(-2) compared with 1.20 Mg km(-2) through the underground outlet. The broader implications of this study are that subsurface and clastic rock sources represent a significant component of the catchment sediment budget, meaning erosion control measures targeting hillslope surface soils alone may have limited impact on suspended sediment export at landscape scale.