While variations of Baltic Sea ice extent and fast ice thickness have been extensively studied, there is little information about the sea ice thickness distribution and its variability. In our study, we quantify the interannual variability of sea ice thickness in the Bay of Bothnia during the years 2003–2016. We use various different data sets: official ice charts, drilling data from the regular monitoring stations in the coastal fast ice zone and from helicopter- and ship-borne electromagnetic soundings. We analyze the different data sets and compare them to each other to characterize the interannual variability, to discuss the ratio of level and deformed ice, and to derive ice thickness distributions in the drift ice zone. In the fast ice zone the average ice thickness is 0.58 ± 0.13 m. Deformed ice increases the variability of ice conditions in the drift ice zone where the average ice thickness is 0.92 ± 0.33 m. In heavily ridged ice regions near the coast, mean ice thickness can be even manyfold thicker than in a pure thermodynamically grown fast ice. Drift ice exhibits larger inter-annual variability than fast ice.