In 2002 to 2006, sediment profile imagery (SPI) was used to study the environmental impact of eutrophication-induced irregular and seasonal hypoxia on marine benthic habitats in six regions in the Skagerrak and Kattegat (West Sweden). The benthic habitat quality (BHQ) was assessed by parameterisation of biogenic structures observed by the SPI technique, and benthic quality status was related to the EU Water Framework Directive (EU-WFD). The temporal changes were analysed by a 5-factor nested ANOVA and significant temporal differences were recorded within three of the regions. Two of these were affected by hypoxia in the deeper parts and one was probably affected by hypoxia below the halocline. The environmental quality status according to the EU-WFD was bad to high in two regions, moderate to good in three regions, and good to high, i.e., acceptable according to the EU-WFD, in only one region. As BHQ is highly correlated to benthic faunal data, measures have to be taken to improve the coastal water quality in five of the six studied areas.