The European Water Framework Directive (WFD) requires the definition of near-natural reference conditions to determine the extent of water bodies' deviation from ``good ecological status'' caused by stress gradients. However, the classification of ecological quality depends on the assessment method applied and the stressor concerned. While assessment methods that are generally applicable would be favourable, many European countries employ the locally developed water quality metrics that assess the impact of organic pollution (including eutrophication) and the associated decrease in dissolved oxygen. These indices do not specifically address stress from organic toxicants, such as pesticides. The aim of this study was to examine the performance of presently used assessment methods to identify reference conditions of non-contaminated streams in five selected European river basins, covering the geographical region from Spain to Finland, as a crucial prerequisite to indicate toxic gradients. The analysis comprised the Belgium biotic index (BBI), the biological monitoring working party (BMWP) scoring system and the revised German saprobic index. For comparison, we included an adaptation of the recently developed SPEAR index. In two previous field studies, this metric highly correlated with measured pesticide gradients. In this study, SPEAR was the only indicator that was generally applicable to all monitoring data and capable of determining ``high ecological status'' of reference conditions in all basins. Thus, based upon previous and own results, the authors suggest the species at risk (SPEAR) index to be potentially useful as a European-wide index to address deviations from ``good ecological status'' due to organic toxicants and recommend it for consideration in integrated water-resource evaluations under the WFD.