Hydropower is considered an important renewable source of energy, but there is substantial criticism concerning conventional hydropower techniques in terms of impaired fish passage and fish damage, as well as aquatic habitat change. An ecologically sustainable hydropower development thus requires improved knowledge on its ecological effects, especially considering novel and emerging techniques that claim to be more “fish friendly” and “ecological”. However, there is a lack of scientifically valid standards for the ecological monitoring of hydropower plants. In the context of the establishment of innovative hydropower techniques in Europe, we developed novel methodological approaches for the comparative evaluation of fish damage and stream ecosystem change that has been validated using case studies that involve different construction types of innovative hydropower techniques. Based on a detailed and standardized protocol for documenting lethal and sublethal types of damage (e.g. fin damage, scale loss, skin wounds), specific patterns of fish injury can be linked with specific power plant components and operating conditions. In addition to the assessment of fish damage, habitat effects and serial discontinuity, considering abiotic variables and aquatic communities (fishes, macroinvertebrates, macrophytes and algae), are quantified following a systematic field sampling design. We propose a multivariate statistical approach to integrate data on fish damage and habitat change for an overall assessment of the ecological effects of hydropower plants. The results of such monitoring can contribute to an objective assessment and comparison of hydropower technologies and may help identify and optimize the ecologically least harmful approaches.