The Water Framework Directive (WFD) requires from member states to monitor hydromorphological features of rivers in order to assess their ecological quality. Thus, numerous hydromorphological assessment methods have been developed with most of them focusing on the dynamics of hydrology, geomorphology and riparian zone extent. Within the scope of this study, we assessed the hydromorphological features of more than 100 river reaches distributed among fourteen WFD River Basin Districts (RBDs) to identify the main drivers of hydromorphological perturbation. We employed the River Habitat Survey (RHS) and we recorded hydromorphological features and modifications in both banks and the channel bed along 500 m for each reach. Then, the Habitat Modification Score (HMS) and the individual sub-scores that indicate the extent of specific modifications (e.g. bridges, fords, weirs, bank reprofiling, bank reinforcement etc) were calculated in order to a) assess the severity of the total artificial modification and b) to highlight the most common and severe causes of longitudinal and cross-sectional alterations. The results showed that alterations such as reprofiling and reinforcement of banks, contributed the most to the total HMS followed by the presence of bridges. Particularly the bank alterations indicate a serious deterioration of the longitudinal profile of the reaches while the occurrence of many small and larger bridges is the main cause for perturbations that affect the stream cross-sectional profile. Overall, these results compile a first nationwide assessment of the hydromorphological status of Greek rivers in line with the WFD and set the basis for further research that will focus on the diversity of stream habitat features as a measure for the overall ecological quality.