In the field of aquatic ecotoxicology, toxicity assessment at molecular level through multi-omics approaches has been primarily conducted in model organisms such as zebrafish and water fleas in laboratory rather than on native species in real-world environments. In this study, we aimed to use a multi-omics platform with non-model domestic species for health assessment by analyzing molecular and biochemical responses. To facilitate omics applications , we established genome database for the swamp shrimp Neocaridina denticulata and the pale chub Zacco platypus. For the toxicity assessment of triclosan (TCS) as an aquatic pollutant, N. denticulata and Z. platypus were exposed to TCS for acute toxicity evaluation. A range of TCS concentrations below LC50 values was determined to reduce mortality effects. We analyzed molecular and biochemical responses at the transcriptomic, proteomic, and metabolomic levels in response to TCS exposure. Finally, we integrated the three omics dataset such as transcriptome, proteome, and metabolome, obtained from the two species exposed to TCS. We found that glutathione metabolism was commonly changed in both species in response to higher concentrations of TCS. Furthermore, N. denticulata exhibited differential expression in carbohydrate metabolism such as glycolysis or starch metabolism, whereas Z . platypus showed significant changes in oxidative phosphorylation. Through the integration of multi-omics datasets, we identified several biomarkers with potential applications in health assessment and further validated their applicability in actual field environments.