Fresh water is a fundamental source for humans, hence the recent shrinkage in freshwater and increase in water pollution are imperative problems that vigorously affect the people and the environment worldwide. The breakneck industrialization contributes to the procreation of substantial abundance of wastewater and its treatment becomes highly indispensable. Perchlorate and nitrate containing wastewaters poses a serious threat to human health and environment. Conventional biological treatment methods are expensive and also not effective for treating wastewater effectively and incapable of in situ bioremediation. Bioelectrochemical systems are emerging as a new technology platform for a sustainable removal of such contaminants from wastewater streams. This article reviews the state of art of bioelectroremediation of contaminated waters with perchlorate and nitrate. Different aspects of this technology such as configuration and design, mode of operation and type of substrate are considered in detail.