The present study was focused on the characterization of the biocenotic diversity of saprotrophic fungi, taking into account the impact of various treatment systems and technological stages as well as the physicochemical properties of wastewater. The biodegradation potential, the hazard posed to humans, animals, and the environment, and the effectiveness of elimination of propagules were evaluated. The most effective elimination of fungal propagules was recorded in hybrid constructed wetland systems with horizontal (HF-CW) and vertical (VF-CW) wastewater flow, especially in the VF-HF objects. The fungal communities present in wastewater from small constructed wetland (CW) and wastewater stabilization ponds (WSP) were dominated by ubiquitous terrestrial molds accompanied by a minimal number of yeasts. The similarity of the species composition of the fungal communities between the treatment plants was generally low, whereas the species diversity together with the population size was very high at the various stages of wastewater treatment. Species with potential pathogenicity to humans and animals accounted for over 45%, i.e., were classified as BioSafety Level 1 and 2 (BSL-1 and BSL-2 groups), and potentially phytopathogenic fungi represented 31.5% of the mycobiota species composition. The dynamics of fungal growth were correlated with the content of organic pollutants and nutrients (nitrogen and phosphorus) and with oxygen deficiency. The accumulation of nitrates corresponded to the decline in the frequency of fungi in treated wastewater. The lowest efficiency of the removal of fungi was exhibited by the biological wastewater stabilization ponds.