According to the European Water Framework Directive coastal ecosystems should be classified by means of their ecological status, assessed from indicators compiled from monitoring data. It has been of primary concern to develop indicators that give clear responses to nutrient enrichment, whereas it has been of less concern that the confidence of an eutrophication assessment may rely on highly uncertain indicators. Indicator bias and precision can be improved by seasonal adjustment and including covariates to account for specific conditions during sampling. The choice of classification approach will have paramount implications for ecological status assessment in case of uncertain indicators, but precision is improved by increasing the number of observations. Analyses of 7 coastal ecosystems showed that residual variation is still large for several of the most commonly used indicators for eutrophication assessment and therefore WFD monitoring requirements will be extensive.