Biologically based wastewater treatment systems are considered a sustainable, cost-effective alternative to conventional wastewater treatment systems. These systems have been used and studied for the treatment of urban sewage from small communities, and recently, it has been reported that they can also effectively remove emerging organic contaminants (EOCs). EOCs are a new group of unregulated contaminants which include pharmaceutical and personal care products, some pesticides, veterinary products, and industrial compounds among others that are thought to have long-term adverse effects on human health and ecosystems. This review is focused on reporting the ability of biologically based wastewater treatment systems to remove EOCs and the main elimination mechanisms and degradation processes (i.e., biodegradation, photodegradation, phytoremediation, and sorption) taking place in constructed wetlands, ponds, and Daphnia and fungal reactors.