Multiple human activities are concentrated along the coasts, causing various physical alterations to hydromorphological (HM) features of coastal ecosystems. We reviewed available knowledge and tools as a basis for the development of a GIS-based pan-European methodology for the assessment of hydromorphological alterations in coastal and transitional waters. We found that there are not many pan-European GIS-based spatial data available to define a baseline for hydromorphological assessment within transitional and coastal waters, although present conditions pressure data are available. Significant number of hydromorphological features of coastal and transitional waters could be assessed using GIS-based data, but combination of various data sources and assessment approaches is needed.