Microbial communities indicate fine differences in pollution levels by emerging contaminants

•Aquatic Quality Index denotes a high impact by emerging contaminants in two coastal lagoon basins from streams to coastal sea.•Microbial communities respond sensitively to emerging contamination at basin scale.•Microbial indicators exhibited a high capacity to predict categories of impacted sites defined by the Aquatic Quality Index.•Molecular indicators based on microbial communities can detect impacts that might otherwise go unnoticed due to their high sensitivity. Aquatic microbial communities are well known to rapidly respond to environmental changes, and to harbor the highest taxonomic and genetic diversity among biological communities. Nevertheless, they remain under-utilized as bioindicators of contamination. Here we applied indicator value analysis (IndVal) to aquatic microbial communities to identify indicators of anthropogenic pressure by emerging contaminants at basin scale. For that, we defined categories of impact according to the Aquatic Quality Index (AQI) based on previous determinations of emerging contaminants (ECs) along an anthropogenic impact gradient. Indicator value analysis (IndVal) was conducted to identify amplicon sequence variants (ASVs; analogous to species in other fields of ecology) associated with each category. It was possible to find combinations of ASV indicators for all impact categories defined by the AQI. Microbial indicators exhibited a high capacity to predict the group membership of the samples within each AQI category and to correctly assign the samples to the appropriate category, employing leave-one-out cross-validation (100 % correctly assigned for streams and coastal sea and 94% for lagoons). This is the first report of emerging contamination indicators based on microbial communities. These results reaffirm the capacity of microbial communities to rapidly adjust their taxonomic composition in response to environmental changes. Therefore, these microscopic entities are promising for the application of environmental management measures and the approximation presented here contributes to the advancement of tools dedicated to monitoring aquatic ecosystems, and the application of more stringent standards for water quality than what is currently implemented.