Estuaries have been suggested to have an important role in reducing the nitrogen load transported to the sea. We measured denitrification rates in six estuaries of the northern Baltic Sea. Four of them were river mouths in the Bothnian Bay (northern Gulf of Bothnia), and two were estuary bays, one in the Archipelago Sea (southern Gulf of Bothnia) and the other in the Gulf of Finland. Denitrification rates in the four river mouths varied between 330 and 905 μmol N m⁻² d⁻¹. The estuary bays at the Archipelago Sea and the Gulf of Bothnia had denitrification rates from 90 μmol N m⁻² d⁻¹ to 910 μmol N m⁻² d⁻¹ and from 230 μmol N m⁻² d⁻¹ to 320 μmol N m⁻² d⁻¹, respectively. Denitrification removed 3.6–9.0% of the total nitrogen loading in the river mouths and in the estuary bay in the Gulf of Finland, where the residence times were short. In the estuary bay with a long residence time, in the Archipelago Sea, up to 4.5% of nitrate loading and 19% of nitrogen loading were removed before entering the sea. According to our results, the sediments of the fast-flowing rivers and the estuary areas with short residence times have a limited capacity to reduce the nitrogen load to the Baltic Sea.