Knowledge on the extent and mechanisms of fish damage caused by hydropower facilities, resulting in direct mortality and delayed effects, is important for their ecological improvement. Herein, we propose a novel field-based method to asses externally visible fish injury combined with a rapid screening of internal injuries using x-ray technology. External injury assessment includes vitality and 4 general health criteria, as well as 9 lethal and sub-lethal injury types across 18 body parts. Additionally, fish are screened for 36 internal injuries using the x-ray protocol. The method was validated using 3.087 specimens from four species of hatchery-reared fish as well as 2.262 specimens from 32 species of wild fish. The external injury protocol allowed a detailed and systematic evaluation of different fish injury types in the field. Injuries related to handling and to contact with different parts of the hydropower structure could be clearly distinguished applying multivariate statistics. The rapid x-ray screening for internal injuries successfully detected injuries of the bony structures, the swim bladder, emboli and haemorrhages and the data could be used to explain delayed mortality within 96h after turbine passage. This approach allows quantifying and comparing external and internal fish injuries across sites, and can help to identify the technologies and operational procedures which minimize harm to fish.