During the Integrated Ocean Drilling Program (IODP) Expedition 347 in 2013, sedimentary records were recovered in the Baltic Sea that cover the Eemian interglacial and Weichselian glacial periods. This non-steady state depositional system was characterized by shifts from limnic to brackish/marine phases over the glacial-interglacial cycle which has subjected the sample location in the Anholt Basin to profound changes in depositional and diagenetic conditions. Here, comprehensive pore-water and solid-phase data of sediments are presented and used to (1) geochemically characterize the different depositional environments, (2) identify key biogeochemical processes and (3) reveal the influence of the abundance and reactivity of metal oxide phases on the cycling of iron, manganese and sulfur and the formation of authigenic iron sulfides across depositional boundaries.