Fungi are essential in wastewater treatment systems and have different taxonomic classifications and adaptation strategies that allow them to thrive under these demanding conditions. The taxonomic diversity of fungi in wastewater treatment includes species such as Aspergillus, Penicillium and Trichoderma, which are known for their effective degradation of organic pollutants. In terms of wastewater, these fungi have the mechanism in them that allows them to survive in high concentration of nutrients and toxic compounds. Among these are the production of extracellular enzymes for the breakdown of high molecular weight organic substrates, the development of thick cell walls that can endure extreme toxic chemical hazards in the surrounding environment, and the ability to form biofilms for effective uptake and also protection from damaging environmental conditions. This chapter covers the fungi and their mechanisms of biological processes and heavy metal binding properties used in the removal of heavy metals and other contaminants from the effluent. The adaptations of the fungi have economic significance in that they allow for low-cost and eco-friendly measures for the treatment of wastewater which is more effective in cleaning contaminants within the water without using much power or producing excess sludges compared to traditional processes based on treatment with bacteria.