Although agriculturally accelerated soil erosion is implicated in the unsustainable environmental degradation of mountain environments, such as in the Himalaya, the effects of land use can be challenging to quantify in many mountain settings because of the high and variable natural background rates of erosion. In this study, we present new long-term denudation rates, derived from cosmogenic 10Be analysis of quartz in river sediment from the Likhu Khola, a small agricultural river basin in the Middle Hills of central Nepal. Calculated long-term denudation rates, which reflect background natural erosion processes over 1000+ years prior to agricultural intensification, are similar to present-day sediment yields and to soil loss rates from terraces that are well maintained. Similarity in short- and long-term catchment-wide erosion rates for the Likhu is consistent with data from elsewhere in the Nepal Middle Hills but contrasts with the very large increases in short-term erosion rates seen in agricultural catchments in other steep mountain settings. Our results suggest that the large sediment fluxes exported from the Likhu and other Middle Hills rivers in the Himalaya are derived in large part from natural processes, rather than from soil erosion as a result of agricultural activity. Catchment-scale erosional fluxes may be similar over short and long timescales if both are dominated by mass wasting sources such as gullies, landslides, and debris flows (e.g., as is evident in the landslide-dominated Khudi Khola of the Nepal High Himalaya, based on compiled data). As a consequence, simple comparison of catchment-scale fluxes will not necessarily pinpoint land use effects on soils where these are only a small part of the total erosion budget, unless rates of mass wasting are also considered. Estimates of the mass wasting contribution to erosion in the Likhu imply catchment-averaged soil production rates on the order of ~ 0.25–0.35 mm yr−1, though rates of mass wasting are poorly constrained. The deficit between our best estimates for soil production rates and measurements of soil loss rates supports conclusions from previous studies that terraced agriculture in the Likhu may not be associated with a large systematic soil deficit, at least when terraces are well maintained, but that poorly managed terraces, forest, and scrubland may lead to rapid depletion of soil resources.