The presence of pharmaceuticals in the environment has led to apparent toxicity with different aquatic species. Clarithromycin, for example, is used in treating respiratory tract infections, has been recently found in the surface waters and rivers which might threaten non-targeted organisms in these matrices. In this study, a model vertebrate Danio rerio (zebrafish) was exposed to 100ppb clarithromycin for 72 hours to evaluate acute toxicity through significantly affected metabolic compounds in the fish’s pathway. Metabolites obtained from q-TOF LC/MS were identified and mapped with the zebrafish’s metabolic pathway using Metlin, and KEGG respectively. 335 compounds are believed to have been significantly altered by the acute exposure of the antibiotic with the fish. The most affected pathways are ABC transporters, steroid hormone biosynthesis, arachidonic acid metabolism, purine metabolism, and biosynthesis of amino acids. With the said findings, it can be concluded that, although concentration of some pharmaceuticals may be as low as the one used in this study, its effects on the aquatic species exposed to it might be significant and should be given immediate attention