Reference total nitrogen (TN) concentrations for the Gardsfjarden estuary in the central Bothnian Sea, which receives discharge from an industrial point-source, have been estimated from diatom assemblages using a transfer function. Sedimentological and diatom evidence imply a good ecological status before 1920 with an assemblage dominated by benthic taxa indicating excellent water transparency, high diatom species richness and less organic sedimentation resulting in homogeneous well oxygenated sediments. A change in the diatom assemblage starts between 1920 and 1935 when the species richness declines and the proportion of planktic taxa increases. Increased organic carbon sedimentation after 1920 led to hypoxic bottom waters, and the preservation of laminae in the sediments. The trend in the reconstructed TN-values agrees with the history of the discharge from the mill, reaching maximum impact during the high discharge between 1945 and 1990. The background condition for TN in Gardsfjarden is 260-300 mu L-1, reconstructed until 1920.