Our study focused on freshwater fungal diversity, an important aspect in assessing the ecology of aquatic ecosystems. We carefully explored the diversity and influencing factors of culturable fungi across Dianchi Lake, Fuxian Lake, Xingyun Lake, and Yangzonghai Lake in Yunnan Province, China. Through fungi culture, morphological characterization, and ITS sequence analysis, we identified a total of 565 isolates belonging to 405 species across 133 genera. The diversity indices viz. H′, D, and J were evaluated for fungal diversity across the lakes. Interestingly, although diversity indices were highest during summer and at Yangzonghai Lake, no significant differences in fungal community diversity were observed between seasons and regions. Water variables were analyzed and indicated that changes with rapid fluctuations in temperature, pH, and dissolved oxygen likely influence fungal diversity. These findings significantly contribute to our understanding of fungal communities within plateau lake ecosystems, thereby aiding in managing and conserving vital aquatic resources.