Biotic indices developed to assess the ecological status of coastal waters according to the European Water Framework Directive (WFD) often show discrepancies when they are applied in transitional environments. Although several indices have been widely used in transitional waters throughout Europe, there is still a lack of knowledge about their suitability assessing ecological status. We evaluated the performance of most common used biotic indices and community parameters (e.g. Multivariate AZTI's Marine Biotic Index (M-AMBI), BENTIX, Benthic Opportunistic Polychaetes Amphipods index (BOPA), diversity indices, species richness, abundance) that have been proposed in the scope of WFD, using data of macroinvertebrate community coming from a special case of transitional water body, the highly stratified Ebro estuary. Additionally, we tested their ability to respond to the main pressures affecting the Ebro estuary, the hydrological alteration due to regulation and the pollution pressure due to nutrient enrichment. Estimation of hydrological alteration was based on flow historical data (period from 1913 to 1963), that we assumed as 'hydrological reference conditions' for Ebro estuary. Pollution pressure was estimated by means of PCA analysis including organic and nutrient enrichment related variables, expressed as a synthetic index by PCA factor scores extraction. All the community parameters were able to detect changes in macrofauna composition along the estuarine gradients and were able to differentiate between the impoverished stations and the healthier ones. Regarding indices, the ratings were contradictory and only M-AMBI classified the stations in the correct way. Strong significant correlations were found between indices and metrics and the calculated pressures; nevertheless, these correlations showed a paradoxical result, since increasing hydrological alteration benefited the macrofauna, achieving great complexity. Other identified limitations of biotic indices were the opposite classifications, overestimation of ecological status and low resolution ability. We conclude that for transitional water ecosystems, where each water body has particular characteristics, is difficult the use of 'common biological' assessment tools as the results of this study, among others (more details in discussion section), have demonstrated. Nevertheless, M-AMBI seemed to work in the correct way, so further investigation about its use for transitional waters is necessary. The development of new strategies such as the use of historical data, the use of metrics as a complement for the assessment could be a reliable alternative.