DNA microarray was used to analyze hepatic transcriptional profile of male mice (Mus musculus) after the mice were fed with Yangtze River (China) source water (NJS) and tap water (NJT) for 90 d. Chemical analysis demonstrated that NJS and NJT contained various trace-level pollutants including polycyclic aromatic hydrocarbons, phthalate ethers and inorganic contaminants. DNA microarray revealed occurrence of 5,042 differentially expressed genes (DEGs) in the mice fed with NJS and 828 DEGs in the mice fed with NJT, indicating that NJS posed greater influence on liver transcriptome. Annotation against Kyoto Encyclopedia of Genes and Genomes pathway database showed that the DEGs in NJS group were mostly involved in lipid metabolism (51 DEGs), followed by neurodegenerative diseases (47 DEGs), energy metabolism (41 DEGs) and endocrine system (38 DEGs). NJT exposure was found to affect lipid metabolism (14 DEGs), xenobiotics biodegradation and metabolism (6 DEGs), and cofactors and vitamins metabolism (5 DEGs). Annotation against Gene Ontology database confirmed that lipid metabolism among the altered pathways was most susceptible to both NJS and NJT exposure. The DEGs were involved in 6 lipid metabolic pathways including fatty acid metabolism, glycerophospholipid metabolism, unsaturated fatty acid biosynthesis, steroid biosynthesis, primary bile acid biosynthesis and steroid hormone biosynthesis. Although both NJS and NJT might cause no obvious liver tissue damages, the lipid metabolic disturbance induced by trace-level pollutants still deserves public health concern.