Regular assessment of surface waters to monitor ecological quality has become an increasing priority in recent years. Stream water quality assessment conventionally relies on taxonomic expertise, which can be costly and time-consuming. Next-generation sequencing approaches for high-throughput analyses of diverse ecosystems are increasingly used for environmental monitoring, and it has recently been shown that this methodology has a large potential for stream water quality assessments. In the present study we assess the potential of an amplicon sequencing based approach that simultaneously targets the 16S (prokaryotes) and 18S (eukaryotes) rRNA genes to capture a snapshot of the in the entire ecosystem composition. Results based on the analysis of 50 selected Danish streams showed that the domain-specific profiles can separate the samples into their respective ecological quality categories. Furthermore, it was possible to extract potential indicator organisms from all three domains associated to a single ecological status category, low and high quality ecosystems, as well as those with a high correlation to ecological status across all categories.