A combination of mineralogical (SEM–EDS, EMPA) and geochemical (redox dynamics, selective extractions) approaches was applied to mining- and smelting-impacted sediments from Lake Uru Uru and from the Cala Cala Lagoon, a non-impacted reference site, in the Bolivian Altiplano. The purpose was to assess the factors controlling the post-depositional redistribution (mobilization/sequestration) of trace metals and metalloids. As expected, trace metals and metalloids are less reactive at the reference site than in Lake Uru Uru. In the latter, trace metals and metalloids are principally hosted by Fe- and Mn-oxyhydroxides, authigenic sulfides and silicate particulates. Post-depositional redistribution is ascribed to early diagenetic processes driven by organic matter (OM) mineralization, including dissolution of trace metal-bearing phases and precipitation of authigenic sulfide and carbonate phases. Seasonal climate variability exerts a strong influence on these processes. Evaporation of surface water during the dry season in the northern part of Lake Uru Uru promotes large redox front oscillations in the sediments and, therefore, transient redox conditions, likely leading to the weakening of anoxia in near-surface sediments and to a ‘compressed’ redox zonation compared to the southern part of the lake. Seasonal disappearance of the water column in the Northern Lake Uru Uru entails an alternation of: (i) low trace element mobility in the dry season due to elemental precipitation; and (ii) an increase of trace element mobility via diffusive transport during the wet season due to release from OM, Fe- and Mn-oxyhydroxides and carbonates upon mineralization, reductive dissolution and destabilization processes, respectively. Reoxidation of authigenic Fe-sulfides likely following the re-instalment of the water column above the sediment at the end of the dry season and prior to the return of anoxia probably favors transport of trace elements to the water column. As a consequence of this intricate web of redox- and climate-related processes, both northern and southern sediments of Lake Uru Uru are a source of dissolved trace elements, particularly As and Cd, for the overlying water column via diffusive transport. However, much of the diffused As and Cd is likely to be removed from the dissolved phase by the redox loop through Fe-oxyhydroxide precipitation. Finally, it is suggested that long term sequestration of trace metals and metalloids in the sediments could be controlled by inter-annual climate variability such as ENSO events.