Many marine algae are strong accumulators of halogens. Commercial iodine production started by burning seaweeds in the 19th century. The high iodine content of certain seaweeds has potential pharmaceutical and nutritional applications. While the metabolism of iodine in brown algae is linked to oxidative metabolism, with iodide serving the function of an inorganic antioxidant protecting the cell and thallus surface against reactive oxygen species with implications for atmospheric and marine chemistry, rather little is known about the regulation and homoeostasis of other halogens in seaweeds in general and the ecological and biological role of marine algal halogenated metabolites (except for organohalogen secondary metabolites). The present review covers these areas, including the significance of seaweed-derived halogens and of halogens in general in the context of human diet and physiology. Furthermore, the understanding of interactions between halogenated compound production by algae and the environment, including anthropogenic impacts, effects on the ozone layer and global climate change, is reviewed together with the production of halogenated natural products by seaweeds and the potential of seaweeds as bioindicators for halogen radionuclides.