Metabolic pathways are targets of environmental contaminants throughout biodiversity. However, due to the lack of available genomic data in many environmental sentinel species, the systematic reconstruction of their metabolic pathways remains limited. It is thus essential to gain a better picture of the metabolism of sentinel species in order to improve our understanding of pollution impacts on the ecosystems. In this study, we used a multi-omics approach to reconstruct the metabolic network of Gammarus fossarum and map the main metabolic pathways expressed in the cephalon, gills, caeca, intestines and male and female gonads. We performed a de novo assembly of RNA-seq data from a previous study and acquired new shotgun proteomic data from male and female G. fossarum organs. The new transcriptome assembly reduced RNA contaminants and transcript redundancy allowing the adaptation of the genomic tool CycADS for metabolic pathway reconstruction to the transcriptomic data. Additionally, we integrated proteomic data and analyzed the expression profile in organs to identify organ-specific metabolic profiles. This dataset contains the de novo transcriptome assembly, proteomic and functional annotation data for Gammarus fossarum, together with the reconstructed metabolic networks of the GamfoCyc metabolic database (available in the ArthropodaCyc collection) and integrated mass spectrometry data.