The introduction of the first list of priority pathogenic fungi by the World Health Organization stresses the need to research and develop public health actions to mitigate infections caused by fungi. One of those actions involves the water disinfection systems, which comprise classical and alternative methods that have been developed in the last decades. Thereby, this work reviews the disinfection of fungi by classical methods such as chlorination, ozonation, and ultraviolet (UV) treatments and alternative advanced oxidation processes (AOPs) such as photo-Fenton, photocatalysis, or couplings of UV with peroxides. The matrices of aquatic systems (sewage, groundwater, drinking water, among others) were considered. A bibliometric analysis is performed initially, and then some aspects of the resistance to antifungals are presented, and the efficiency of the diverse processes in the reduction in fungal loading is also revised. Herein, it is shown the role of the disinfecting agents (e.g., chlorine, hydroxyl radical, or light) and their effects on fungi structures (e.g., direct DNA damage, or indirect damage due to the action of radicals). Moreover, gaps, such as the treatment of antifungal-resistant fungi and limited information about combinations among AOPs, related to the disinfection of water polluted by fungi, were identified.