High-throughput sequencing was employed to characterize pathogenic fungal communities in soil, groundwater, bioaerosols, and waste pile samples from a typical municipal landfill. The relative abundance of soil-borne pathogenic fungi was significantly higher downstream of the landfill (30.33 %) than upstream (18.75 %), which suggests that the landfill poses more risk to biosafety downstream than upstream. Dominant genera in surface layers and vadose zones included Pseudallescheria, Pichia, Alternaria, Perconia, Bisifusariu, and Fusarium, comprising 84.04 % of pathogenic fungi, while Malassezia, Aureobasidium, and Trichoderma prevailed in deeper phreatic aquifer and bottom layers. Coupled multi-media transport analysis revealed that both leachate-driven groundwater transport and aerosol deposition contributed to the pathogenic fungal load in soils. Variance partitioning analysis (VPA) revealed that environmental factors explained 43.6 % of fungal community variation. Redundancy analysis (RDA) and Canonical correspondence analysis (CCA) revealed that cation exchange capacity (CEC), pH, infiltration, and moisture were the primary environmental drivers shaping fungal communities. Heavy metals concentrations (Cu, As, Cd) have strong correlation with many pathogenic fungi and shared a similar distribution pattern. These findings highlight the landfill’s role in disseminating pathogenic fungi, posing elevated biosafety risks to the surrounding soil, and necessitating enhanced monitoring and mitigation.