Efforts to increase the share of renewable energies and to reduce the negative ecological impacts of hydropower use are driving the development of novel hydropower technologies. Innovative hydropower concepts and turbine types should cause less fish damage and be more ‘eco-friendly’ than conventional hydropower plants. In this study, extensive ecological monitoring at the world's first innovative shaft hydropower plant (SHPP) was carried out. The monitoring included the assessment of the corridor usage of downstream moving fish, turbine-related fish injuries and mortality, as well as changes in aquatic community and habitat associated with hydropower plant construction in a before-after comparison. A large proportion of downstream moving fish was not prevented from turbine passage by the installed physical barrier, resulting in mortality rates up to 44% that can be similar to those at conventional Kaplan turbines. Strike and pressure changes (decompression rate up to 377 kPa/s) during turbine passage were identified as a major cause of mortality. In addition, significant differences in the aquatic community and abiotic habitat characteristics between upstream and downstream sides of the dam could be detected, indicating an interruption of the river continuum. The findings of this study indicate that the theoretical advantages of the SHPP concept of optimal fish protection from turbine passage and a low disruption of the serial continuity could not be realized in practice. Further research is needed to optimize this concept to better prevent fish from turbine entrainment, improve bypass efficiency and reduce the effects of the disruption of serial continuity.