Due to increased freshwater demand across the globe, seawater desalination has become the technology of choice in augmenting water supplies in many parts of the world. The use of chemical disinfection is necessary in desalination plants for pre-treatment to control both biofouling as well as the post-disinfection of desalinated water. Although chlorine is the most commonly used disinfectant in desalination plants, its reaction with organic matter produces various disinfection by-products (DBPs) (e.g., trihalomethanes [THMs], haloacetic acids [HAAs], and haloacetonitriles [HANs]), and some DBPs are regulated in many countries due to their potential risks to public health. To reduce the formation of chlorinated DBPs, alternative oxidants (disinfectants) such as chloramines, chlorine dioxide, and ozone can be considered, but they also produce other types of DBPs. In addition, due to high levels of bromide and iodide concentrations in seawater, highly cytotoxic and genotoxic DBP species (i.e., brominated and iodinated DBPs) may form in distribution systems, especially when desalinated water is blended with other source waters having higher levels of organic matter. This article reviews the knowledge accumulated in the last few decades on DBP formation during seawater desalination, and summarizes in detail, the occurrence of DBPs in various thermal and membrane plants involving different desalination processes. The review also identifies the current challenges and future research needs for controlling DBP formation in seawater desalination plants and to reduce the potential toxicity of desalinated water.