Barium (Ba) isotopes are a promising new tracer for riverine freshwater input to the ocean and marine biogeochemical cycling. However, many processes that affect Ba cycling at continental margins have not yet been investigated with respect to Ba isotope fractionation. Here, we present Ba concentration and isotope data for water column, pore water and sediment samples from Kiel Bight, a seasonally stratified and hypoxic fjord in the southwestern Baltic Sea. As expected for such a brackish, marginal sea, the water column Ba inventory and its isotopic composition can be explained by mixing of riverine freshwater and Atlantic seawater. However, the deep water below the seasonal pycnocline is characterized by a pronounced positive Ba concentration anomaly (up to 915 nM) that is accompanied by a δ¹³⁸Ba (+0.23 ‰) lighter than expected from the seawater-freshwater mixing line (Ba: 77 nM, δ¹³⁸Ba: +0.32 ‰ at a salinity of 18). Pore water profiles indicate a Ba flux across the sediment-water interface, which contributes to the enrichment of isotopically light Ba in the deep water. Pore waters of surface sediments and deep waters are oversaturated with respect to barite. Therefore, barite dissolution is unlikely to account for the benthic Ba flux. Water column Ba concentrations closely correlate with those of the nutrients phosphate and silica, which are removed from surface waters by biological processes and recycled from the sediment by diffusion across the sediment-water interface. As nutrient-to-Ba ratios vary among the different sites, we propose that Ba is removed from surface waters by adsorption onto biogenic particles (rather than assimilation) and regenerated within surface sediments upon organic matter degradation. Isotope fractionation during Ba uptake in the water column is best explain by a closed system Rayleigh model with an isotope fractionation factor Δ¹³⁸Ba_{dissolved-particulate} of +0.07 ‰. Our findings provide new constraints on how sedimentary processes may affect the Ba isotope composition of coastal and near bottom seawater.