Although most of the EU members have adopted methods for assessing the hydromorphological quality of lotic ecosystems in line with the Water Framework Directive, until now, Greece lacked an integrated approach. In this article, we present the results of the first nationwide assessment of habitat quality for rivers in Greece, using the River Habitat Survey (RHS) alongside a typology of Greek rivers. The RHS toolbox software has been updated with data from the Greek monitoring program which allowed for type-specific assessments using the Habitat Quality Assessment (HQA) score. The HQA scores from 366 monitoring sites were analyzed to identify spatial patterns and significant variations. Sites were classified in five HQA classes based on the position of their HQA score relative to sites of similar types. We also investigated whether Ecological Quality Ratios (EQRs) for three biological quality elements (benthic diatoms, benthic macroinvertebrates and fish) differed significantly among HQA classes. Correlations showed that sites at mid and high altitude catchments with natural land cover had better HQA scores than lowland sites with agricultural land cover. In addition, large urbanized districts (e.g. Attica), and central Greece displayed lower habitat quality than Epirus and Western Macedonia. Our findings revealed that EQR values varied significantly among the HQA classes, with these differences being more prominent for small and medium lowland streams. This study shows that this approach can identify sites that are prone to habitat degradation and require further management, whilst providing a consistent framework for exploring the relationships between biota and hydromorphological conditions.