Within the research and development project “Alternative technical-biological bank protection measures on Federal Waterways”, ecological alternatives to technical bank protection methods are investigated by the German Federal Waterways Engineering and Research Institute (BAW) and the German Federal Institute of Hydrology (BfG) to advise the Federal Waterways and Shipping Administration (WSV) in order to meet the requirements of the European Water Framework Directive (WFD). Different bank protection measures have been implemented and analyzed for their ecological potential. They are examined on different types of Federal Waterways. Characteristic floristic and faunistic parameters and their performance regarding ecosystem services were examined under varying navigation intensities and different water levels. Up to now, several alternative bank protection measures developed well and resisted increasing navigation induced impacts, such as permanent flooding and wave dynamics. In particular, measures, including the implementation of willow brush mattresses, willow branch cuttings and if possible bank flattening and reed planting, showed most efficient ecological solutions above mean water. With regard to the development of species according to the WFD within the aquatic zone and the amphibian zone, alternative bank protection measures need to be applied more strictly underneath the mean water level to increase the ecological potential and the near-natural development on federal waterways in Germany.