Natural nanoparticles (NNPs) in rivers, lakes, oceans and ground water predate humans, but engineered nanoparticles (ENPs) are emerging as potential pollutants due to increasing regulatory and public perception concerns. This Review contrasts the sources, composition and potential occurrence of NNPs (for example, two-dimensional clays, multifunctional viruses and metal oxides) and ENPs in surface water, after centralized drinking water treatment, and in tap water. While analytical detection challenges exist, ENPs are currently orders of magnitude less common than NNPs in waters that flow into drinking water treatment plants. Because such plants are designed to remove small-sized NNPs, they are also very good at removing ENPs. Consequently, ENP concentrations in tap water are extremely low and pose low risk during ingestion. However, after leaving drinking water treatment plants, corrosion by-products released from distribution pipes or in-home premise plumbing can release incidental nanoparticles into tap water. The occurrence and toxicity of incidental nanoparticles, rather than ENPs, should therefore be the focus of future research.