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. We present a comprehensive data set of 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.