Abstract. The management of sediment and other non-point source (NPS) pollution has proven difficult, and requires a sound understanding of particle movement through the drainage system. The primary objective of this investigation was to obtain an understanding of NPS sediment source(s), transport, and storage within the Mkabela Basin, a representative agricultural catchment within the KwaZulu–Natal Midlands of eastern South Africa, by combining geomorphic, hydrologic and geochemical fingerprinting analyses. The Mkabela Basin can be subdivided into three distinct subcatchments that differ in their ability to transport and store sediment along the axial valley. Headwater (upper catchment) areas are characterized by extensive wetlands that act as significant sediment sinks. Mid-catchment areas, characterized by higher relief and valley gradients, exhibit few wetlands, but rather are dominated by a combination of alluvial and bedrock channels that are conducive to sediment transport. The lower catchment exhibits a low-gradient alluvial channel that is boarded by extensive riparian wetlands that accumulate large quantities of sediment (and NPS pollutants). Fingerprinting studies suggest that silt- and clay-rich layers found within wetland and reservoir deposits of the upper and upper-mid subcatchments are derived from the erosion of fine-grained, valley bottom soils frequently utilized as vegetable fields. Coarser-grained deposits within these wetlands and reservoirs result from the erosion of sandier hillslope soils extensively utilized for sugar cane, during relatively high magnitude runoff events that are capable of transporting sand-sized sediment off the slopes. Thus, the source of sediment to the axial valley varies as a function of sediment size and runoff magnitude. Sediment export from upper to lower catchment areas was limited until the early 1990s, in part because the upper catchment wetlands were hydrologically disconnected from lower parts of the watershed during low to moderate flood events. The construction of a drainage ditch through a previously unchanneled wetland altered the hydrologic connectivity of the catchment, allowing sediment to be transported from the headwaters to the lower basin where much of it was deposited within riparian wetlands. The axial drainage system is now geomorphically and hydrologically connected during events capable of overflowing dams located throughout the study basin. The study indicates that increased valley connectivity partly negated the positive benefits of controlling sediment/nutrient exports from the catchment by means of upland based, best management practices.