Arsenic, antimony, and germanium species concentrations have been determined from five hydrographic stations along the central axis of the Baltic Sea from the Bornholm Basin to the Gulf of Finland. Arsenic and antimony concentrations are lower than in the open oceans and in most rivers. In the oxic waters, the pentavalent species of As and Sb predominate, while in the anoxic basins, the distribution shifts to the trivalent species and possibly some sulfo‐complexes. Methylated arsenic species make up a large fraction of dissolved As in the surface waters, and methylated species of As, Sb, and Ge are detectable throughout the water column. Germanic acid concentrations are about ten times higher than in the ocean and much higher than can be accounted for by fluvial input. The vertical distributions of arsenic, antimony, and germanium within the Baltic Sea are controlled by biogeochemical cycling, involving biogenic uptake, particulate scavenging and partial regeneration. A mass balance including river and atmospheric inputs, exchange with the Atlantic through the Belt Sea, and removal by sediment deposition suggests that anthropogenic inputs make a significant contribution to the budgets of all three elements, with atmospheric fluxes dominating the input of Ge to the Baltic.