The European Water Framework Directive (WFD) requires the definition of reference conditions, i.e. pristine conditions, for all surface waters. As the present state of Danish coastal waters cannot be referred to as pristine, reference conditions have to be assessed by analysis of historical data or by the use of models. Using Randers Fjord as an example, the aim of this work was i) to demonstrate possibilities and restrictions of assessing reference conditions by historical data and by modelling; and ii) to demonstrate how ecological conditions have changed along with eutrophication. The ample historical data from Randers Fjord allowed us to assess reference conditions with respect to benthic macrophytes and benthic fauna. Models of varying complexity enabled us to assess reference conditions for nutrients, chlorophyll a, Secchi depth, and eelgrass. We conclude that models can be a useful supplement to assess reference conditions, though they are presently restricted by the lack of quantitative links between eutrophication and species composition.