The application of mass spectrometry imaging (MSI) is a promising tool to analyze the spatial distribution of organic contaminants in organisms and thereby improve the understanding of toxicokinetic and toxicodynamic processes. MSI is a common method in medical research but has been rarely applied in environmental science. In the present study, the suitability of MSI to assess the spatial distribution of organic contaminants and their biotransformation products (BTPs) in the aquatic invertebrate key species Gammarus pulex was studied. Gammarids were exposed to a mixture of common organic contaminants (carbamazepine, citalopram, cyprodinil, efavirenz, fluopyram and terbutryn). The distribution of the parent compounds and their BTPs in the organisms was analyzed by two MSI methods (MALDI- and DESI-HRMSI) after cryo-sectioning, and by LC-HRMS/MS after dissection into different organ compartments. The spatial distribution of contaminats in gammarid tissue could be successfully analyzed by the different analytical methods. The intestinal system was identified as the main site of biotransformation, possibly due to the presence of biotransforming enzymes. LC-HRMS/MS was more sensitive and provided higher confidence in BTP identification due to chromatographic separation and MS/MS. DESI was found to be the more sensitive MSI method for the analyzed contaminants, whereas additional biomarkers were found using MALDI. The results demonstrate the suitability of MSI for investigations on the spatial distribution of accumulated organic contaminants. However, both MSI methods required high exposure concentrations. Further improvements of ionization methods would be needed to address environmentally relevant concentrations.