Uranium (U) isotopic signatures and concentration in sediments are widely used as paleo-redox proxies, as the behavior of U is often controlled by bottom water oxygenation. Here, we investigated the processes controlling U accumulation in the sediments of Lake Nègre (Mediterranean Alps, South-East France) over the past 9200 years. Exceptionally high natural U concentrations (350–1250 μg·g−1) allowed the measurement of U along with other elements by high-resolution X-Ray Fluorescence core-scanning. Weathering and erosion proxies (Ti content, Zr/Al and K/Ti ratios) indicate that sedimentary inputs were controlled by Holocene climatic variations. After a period of low erosion during the Holocene Climatic Optimum, a major regime shift was recorded at 4.2 kyr BP when terrigenous fluxes consistently increased until present with high sensitivity to centennial-scale climatic events. Sedimentary organic matter (OM) inputs were dominated by terrigenous OM from the catchment soils until 2.4 kyr BP, as attested by carbon to nitrogen (C/N) and bromine to organic carbon (Br/TOC) ratios. From 2.4 kyr BP to present, lake primary production and soils equally contributed to sedimentary OM. Uranium fluxes to the sediments were well correlated to terrigenous OM fluxes from 7 kyr BP to present, showing that U supply to the lake was controlled by U scavenging in the soils of the watershed followed by transport of U bound to detrital organic particles. Higher U/OM ratios before 7 kyr BP likely reflect the development of the upstream wetland. The fluctuations of U sedimentary inputs appear to be independent of bottom water oxygenation, as estimated from constant Fe/Mn ratios and δ238U isotopic signatures, and rather controlled by the production, erosion and sedimentation of terrigenous OM. This finding confirms that the use of U (and potentially other metals with high affinity to OM) concentrations alone should be used with caution for paleo-redox reconstructions.