Sedimentary molybdenum (Mo) and uranium (U) enrichments have been widely used as a proxy for redox conditions in oxygen-depleted marine paleo-environments. However, in a dynamic upwelling system the seasonal fluctuations from oxic to completely anoxic-sulfidic bottom waters and lateral sediment transport can modify the primary Mo and U signal of the sediment, which in turn may impact paleo-redox interpretations. In this study we present pore water and solid phase data collected at two cross shelf transects during the ‘more oxygenated’ austral winter and ‘anoxic’ austral summer to study the influence of spatially and seasonally contrasting redox conditions on the formation of authigenic Mo and U enrichments in organic carbon (TOC) rich mud belt sediments on the Namibian shelf. A mass balance was established for each element based on diffusive fluxes and element mass accumulation rates to evaluate the respective mechanisms of trace metal delivery, accumulation and recycling.Mo is delivered to the sediment in its dissolved form via diffusion across the sediment–water interface, especially during austral summer when bottom waters are anoxic and surface sediments are highly sulfidic. In the center of the inner shelf mud belt, the benthic Mo fluxes of up to 37 nmol cm−2 yr−1 into sulfidic surface sediments are the highest ever reported for reducing sulfidic systems and agree with the rate of Mo accumulation in the solid phase. Concurrently, high sedimentation rates and low terrigenous input limit solid phase Mo accumulation on the Namibian shelf. In ancient marine sediments, this mode of Mo cycling can be identified by low Mo/TOC ratios of ∼2 similar to those found in sediments deposited below the perennial oxygen minimum zone on the Peruvian shelf and to those found in deposits of the Cretaceous Oceanic Anoxic Event 2. Diffusive U fluxes into the sediment are generally too low to account for the sedimentary enrichment leading to the conclusion that U is delivered mainly in particulate form. In areas with anoxic bottom water, shallow dissolved U maxima directly below the sediment water interface and rather low sedimentary U content indicate that particulate U is recycled and largely released back into the bottom water. At sites where bottom water oxygen concentrations vary from anoxic to completely oxic on seasonal timescales, the depth at which Mo and U are removed from pore waters moves vertically within the sediment column thus defining a layer between the sediment surface and ∼20 cm depth, in which Mo and U accumulate in the solid phase. Our results emphasize the importance of short-term redox fluctuations in the bottom waters and underlying sediments, as well as lateral sediment transport for the authigenic enrichment of redox-sensitive trace metals in reducing shelf sediments. The relative enrichment patterns identified might be useful for the reconstruction of open marine anoxia in the geological past.