Abstract Hydrogen sulfide (H2S) is linked to water quality deterioration in the Baltic Sea, with widespread seafloor hypoxia. We examined the vertical and temporal variability of in situ [H2S], oxygen concentration ([O2]), temperature (T) and pH at weekly, hourly and minute intervals at 13 locations in the western Gulf of Finland in 2013–2014. The main target was the 60–100 m water depth range, containing 3.2–290 μM O2 and 6.3–22.6 μM H2S. Where gas was detected by acoustic surveys, the structure of the H2S layer was more complex compared to stations devoid of gas. Local minima and maxima in pH frequently occurred near the H2S upper boundary (redox transition zone). Except for the homogeneous, tranquil zone above the seafloor at some stations, substantial rapid changes in hydrographic conditions were common. Typically, a layer of marked temporal T variability was present atop or within the topmost H2S layers. The largest temporal changes over a weekly period were − 0.44 °C/− 10.8 μM H2S/− 0.12 pH units (at seafloor level), + 0.18 °C/+7.9 μM H2S between casts (1 h) and + 0.03 °C/− 2.5 μM H2S per minute (high resolution logging). Abrupt [H2S] changes were recorded at two stations with sediments containing free gas. The T and [H2S] changes were synchronous at several layers, reflecting water movement. We conclude that rapid changes occur in hydrographic conditions in the near-bottom H2S layer in the northern Baltic Sea, especially at locations where free gas is present in the underlying sediments.