This dataset presents hydrogen sulfide (H2S) and nitrate (NO3-) concentrations in the water column at 15 stations in the Kiel Bight taken during the research cruises BE10/2018 (23.10.2018), BE03/2019 (15.03.2019), L23-13 (13.09.2023 - 15.09.2023), Hai24VE2 (24.09.2024) and EMB374 (04.09.2025 - 13.09.2025). Water samples were collected using Niskin bottles attached to a stainless-steel framework with CTD sensors. Concentrations of H2S and NO3- were measured photometrically (Hitachi U-2900). The data are used to describe seasonal hypoxia in the Kiel Bight water column and are combined with sediment and porewater data to identify controlling factors governing the accumulation of H2S at the seafloor. Furthermore, we compare the H2S measurements from the deepest Niskin bottle with bottom water H2S concentrations obtained from the benthic tracer profiler and from the overlying water in sediment cores. This allows us to illustrate H2S trends from several meters above the seafloor down to the sediment-water interface, and to discuss advantages and limitations of the different sampling techniques in characterizing geochemical conditions in the benthic environment.