Fish migration is essential to maintain healthy aquatic ecosystems, but hydraulic structures across rivers have impeded natural fish migration worldwide. While efforts have been made to allow fish to pass some hydraulic structures, there is limited understanding of hydrodynamic effects that cause fish injury in different hydraulic systems, such as spillways and stilling basins as well as hydropower systems. This study reviewed available literature on this topic to identify the current knowledge of fish injury thresholds in laboratory- and field-based studies of hydraulic systems. Often, the hydraulic effects that lead to fish injury have been described with time-averaged simplified parameters including shear stress, pressure changes, acceleration, vortical motions, aeration, collision, and strike, while these hydrodynamic effects often occur simultaneously in the turbulent flows across hydraulic structures, making it difficult to link specific fish injuries to a particular hydrodynamic effect. Strong variations of injury may occur, depending on the type and the intensity of hydrodynamic effects, as well as the fish species and fish sizes. Modelling can provide information of stressors, but real-world tests are needed to accurately assess fish injury and mortality. Fish injury mechanisms at hydropower turbines are well understood, however, clear understanding at other sites is lacking. Future studies should aim to report holistic hydrodynamic thresholds with associated fish injury rates. Multidisciplinary systematic research is required, including laboratory and field studies, using passive tracer sensor packages and state-of-the art instrumentation in conjunction with live fish. This can quantify stressors with meaningful parameters, aiming to improve fish safety with more sustainable design of water infrastructure that reduces fish injury when passing across hydraulic structures.