Prechlorination is used in seawater desalination processes to control the biofouling in both thermal desalination plants and membrane desalination plants. A large diversity of disinfection byproducts (DBPs) is formed during seawater pretreatment processes using chlorination, including the regulated trihalomethanes (THMs) and haloacetic acids (HAAs). Nitrogenous DBPs (N-DBPs) generally form in much smaller amounts than regulated DBPs, but have been a growing concern over the past decade because of their greater health risk. High levels of nitrogen-containing compounds in algal organic matter (AOM) can lead to the formation of significant quantities of N-DBPs during algal bloom events. Moreover, the presence of high concentrations of bromide and iodide ion in seawater favors the formation of brominated and iodinated byproducts that are often more toxic than their chlorinated analogues. The aim of this work is to assess the formation and the behavior of halogenated byproducts along the treatment train of full-scale desalination plants. In the first campaign of this work, one thermal multi-stage flash distillation (MSF) plant and one reverse osmosis (RO) plant were studied, both located on the Red Sea coast of Saudi Arabia. Results show that DBPs formed during the pre-chlorination step are efficiently removed along the treatment processes (MSF or RO). Future work will focus on DBPs produced during algal bloom events.