Human land use changes have altered soil erosion for millennia with extensive consequences on terrestrial and aquatic ecosystems as well as biogeochemical cycles in the Critical Zone. Despite its great importance, past erosion fluxes and trends have high uncertainties limiting quantitative estimates to force soil erosion models. Here, we applied a new approach combining well-dated paleo-records of soil erosion and a spatially distributed semi-empirical model to simulate annual soil erosion in six lake watershed systems during the Holocene. Progressive and abrupt changes in soil erosion are detected in the six watersheds. Progressive erosion explains most of the soil exports during the Early Holocene, while abrupt erosion that can be associated with erosion crisis is generally transient, spanning approximately 1000 (± 500) years and mainly occurring during the late Holocene (from 3000 to 1000 cal. yr. BP). Our coupled approach of proxy-model reconstruction shows that the transient erosion crisis represents the half of the total soil erosion exports during the Holocene. These estimates defy current representations of large-scale soil erosion during the Holocene that do not consider transient erosion crisis, hence potentially underestimating the anthropogenic perturbation of lateral fluxes and fate in the Critical Zone. Our results further suggest that erosion and/or land cover proxies need to be consistently integrated into model approaches when attempting to estimate past variations in mass exports from terrestrial to aquatic ecosystems over centennial to millennial timescales.