This paper presents a study of changes in eutrophication over the past 100 years in a fertile estuary. The Danish estuary Mariager Fjord is a long, narrow sill-fjord with a permanently anoxic basin. In 1997 anoxia spread from the basin to the entire inner estuary, killing almost all eukaryotes and prompting debate on the causes. This paper reports a multi-proxy survey of ²¹⁰Pb-dated sediment cores from the anoxic basin. Analyses of diatoms, dinoflagellates, pigments and geochemical proxies were used to determine changes in ecosystem structure over the past 100 years. The aim was to establish ‘base-line conditions', for management purposes, of the biological structure prior to 1900, and to examine possible causes of changes observed. Geochemical proxies total nitrogen (TN), total carbon (TC) and biogenic silica (BSi) were consistently high throughout the sediment record. Increased concentrations of pigments and natural isotopes (d¹³C, d¹⁵N) suggested increasing production and nutrient loading. The main changes in the biological proxies occurred between 1915 and the 1940s, and indicated that the estuary has been somewhat eutrophic since 1900, but that the eutrophication process increased over the past 100 years. A reconstruction of TN concentration by a diatom-based transfer function supports this interpretation, with inferred TN ca. 1900 around 60 µmol l^-1, and an increase in TN concentration over the past century to ca. 130 µmol l^-1 by 1995. Inferred TN decreased to ca. 100 µmol l^-1 by 2001, similar to present day monitoring data.