Sedimentary molybdenum (Mo) and uranium (U) enrichments are often used as redox proxies to reconstruct bottom water redox changes. However, these redox proxies may not be equally reliable across a range of coastal settings due to varying depositional environments. Fjords vary greatly in their depositional conditions, due to their unique bathymetry and hydrography, and are highly vulnerable to anthropogenic and climatic pressures. Currently, it is unknown to what extent Mo and U sequestration is affected by variable depositional conditions in fjords. Here, we use pore water and sequential extraction data to investigate Mo and U enrichment pathways in sediments of two sill fjords on the Swedish west coast with contrasting depositional environments and bottom water redox conditions. Our data suggest that sedimentary authigenic Mo and U pools differ between the two fjords. At the (ir)regularly dysoxic (oxygen = 0.2–2 mL L−1) Gullmar Fjord, authigenic Mo largely binds to manganese (Mn) oxides and to a lesser extent to iron (Fe) oxides; Mo sulfides do not play a major role due to low sulfate reduction rates, which limits the rate of Mo burial. Authigenic U largely resides in carbonates. At the (ir)regularly euxinic (oxygen = 0 mL L−1; total hydrogen sulfide ≥ 0 mL L−1) Koljö Fjord, authigenic Mo is significantly higher due to binding with more refractory organic matter complexes and Mo-Fe-sulfide phases. Uranium is moderately enriched and largely bound to organic matter. We found no direct evidence for temporal changes in bottom water redox conditions reflected in Mo and U enrichments at either Gullmar Fjord or Koljö Fjord. While sulfidic bottom waters favor Mo sequestration at Koljö Fjord, enrichment maxima reflect a combination of depositional conditions rather than short-term low-oxygen events. Our data demonstrate that secondary pre- and post-depositional factors control Mo and U sequestration in fjords to such an extent that bottom water redox conditions are either not being systematically recorded or overprinted. This explains the large variability in trace metal enrichments observed in fjords and has implications for applying Mo and U as proxies for environmental redox reconstructions in such systems.