​Many human activities are concentrated along the coasts, causing various physical alterations to hydromorphological features. Physical alterations to hydromorphological features need to be assessed in a harmonized way across the European coastal zones to support ecosystem-based integrated management and to maintain human well-being. Assessment of relevant hydromorphological features in selected coastal areas using GIS-based data is one of the key steps toward development of a pan-European assessment method. We developed a GIS-based method for quantitative scoring of hydromorphological features for coastal waters using large-scale assessment units. European Environmental Agency grid was found as most appropriate for large-scale hydromorphological assessment of the European coastal waters. Assessment zones were defined and scoring method developed for coastal water hydromorphological features on non-tidal (< 1 m) waters. Adriatic Sea was chosen as testing area. Hydromorphological assessment of the Adriatic Sea coastal waters was performed using data from varied sources: Copernicus Coastal zone land cover/land use, EMODnet, Free flowing rivers, and Copernicus Marine data. The assessment of each hydromorphological feature is based on the comparison of current conditions with the baseline conditions. For some hydromorphological features; however, it is assumed that baseline conditions represent absence of artificial structures, urban areas, human activities, or presence of natural flow conditions, whereas for other we took oldest available and comparable GIS-based data. Altogether, seven generic hydromorphological features were assessed. For all features were developed quantitative scoring criteria. Varied number of selected hydromorphological generic features were scored in potential assessment areas of the Adriatic Sea. However, all seven considered generic features were scored in 183 assessment cells. Generally, generic features of coastal zone morphology showed poorer conditions in comparison to features of hydrodynamic regime. Differences in observed conditions among hydromorphological generic features might be partially due to varied baseline conditions as appropriate data from the past are limited. We used baseline approach and GIS-based data, however, there are still some challenges in the assessment of hydromorphological features of coastal waters. Additional upgrade of data mappings and cross-service activities might enable improved assessment of hydromorphological conditions of coastal waters at a pan-European scale.