Fish are important sentinel organisms for the assessment of water quality and play a central role in ecotoxicological research. Of particular importance to the assessment of health and fitness of fish stocks in response to environmental conditions or pollution are morphometric (e.g. Fulton's condition index) and somatic indices (e.g. hepatosomatic, and gonadosomatic index). Standard measurements of somatic indices are invasive and require, by definition, the sacrifice of examined animals, thus prohibiting longitudinal studies and relocation of animals captured in the field. As a potential solution, in the present study, we propose the use of micro-computed tomography (μCT) as imaging modality to non-invasively tomographically image rainbow trout (Oncorhynchus mykiss) exposed to different sediment suspensions. We here demonstrate that μCT can be used as a tool to reliably measure the volumes of different organs, which could then be applied as a substitute of their weights in calculation of somatic indices. To the best of our knowledge, this study is the first to report the results of μCT analyses in the context of ecotoxicological research in rainbow trout. It has the potential to greatly increase the information value of experiments conducted with fish and also to potentially reduce the number of animals required for studying temporal effects through facilitating longitudinal studies within the same individuals.