The increased pollution in ecosystems reinforces the importance of both chemical monitoring and biological monitoring of streams and rivers, as an effective water quality-based approach to assess aquatic ecosystem health. In this study, gudgeon (Gobio gobio) and mullet (Mugil cephalus) liver histopathology (biomarker) and some macroinvertebrate community indexes and metrics (bioindicator) were used to evaluate the effect of the wastewater treatment plant (WWTP) of Febros (Avintes) in Febros River water quality and ecosystem health. Regarding macroinvertebrate communities, the Belgian Biotic Index (BBI) and Iberian Biological Monitoring Working Party (IBMWP) indexes suggested that Febros water was slightly polluted, even though the worst situation was found downstream the WWTP discharge. Concerning community metrics, upstream percent of individuals in five numerically dominant taxa (80%) was slightly more superior than the downstream (78%). The presence of intolerant or sensible individuals, determined by percent of Ephemeroptera, Plecoptera, and Trichoptera individuals and number of Ephemeroptera, Plecoptera, and Trichoptera families metrics, was higher upstream WWTP, reflecting a better water quality. The histopathology shows the presence of hepatic lesions in gudgeon and mullet. The statistical analysis of the lesion gradation showed that only necrosis was significantly higher in gudgeon captured downstream the WWTP, while differences were not observed for mullet. The multivariate analysis of data confirmed the existence of differences in hepatic lesions between gudgeon and mullet and between sampling sites. Regarding macroinvertebrate community, this analysis showed that the organic contamination reflected by the BBI and IBMWP indexes values was a determinant factor in the spatial distribution of macroinvertebrates. This work showed that the study of different biological organization levels can be used for a better assessment of ecosystem ecological integrity and can be used as a tool to reveal anthropogenic activity effects in macroinvertebrate diversity and in fish liver pathology from Febros River.