Drinking water is an important natural resource. For many people worldwide, especially in developing countries, access to safe drinking water is still a dream. An increasing number of human activities and industrialization have caused various physical, chemical, and biological pollutants to enter water bodies, affecting human health. Water pollutants contain a vast number of additives, such as perfluorinated chemicals, polybrominated diphenyl ethers, phthalate, nanomaterials, insecticides, microcystins, heavy metals, and pharmacologies. In this work, we aim to explore the potential relationship between water pollutants and human diseases. Here, we explored an integrative approach to identify genes, biological processes, molecular functions, and diseases linked to exposure to these water pollutants. These processes and functions affected by water pollutants are related to many diseases, including colonic neoplasms, breast neoplasms, hepatitis B, bladder cancer, and human cytomegalovirus infection. In addition, further analysis revealed the genes that play a key role in the human diseases induced by water pollutants. Therefore, conducting an integrative toxicogenomic analysis of water pollutants is more appropriate for evaluating the potential effects of water pollutants on human health.