Significant lake shrinkage in arid and semi-arid regions has profoundly altered microbial communities crucial to biogeochemical cycles. This study characterized fungal diversity and community structure across 10 saline-alkaline lakes on the Ordos Plateau, China, using internal transcribed spacer rRNA gene amplicon sequencing. The lakes spanned a salinity gradient (0.34-431 g l-1), alkaline conditions (pH 8.51-10.25), and elevated Na+, Cl-, CO32-, and SO42- concentrations. Ascomycota dominated the fungal communities (58.32%), followed by Basidiomycota (7.63%) and Mucoromycota (2.04%), while 31.54% of operational taxonomic units remained unclassified, indicating substantial undocumented fungal diversity. Both fungal alpha diversity (Shannon index: 1.9-4.62) and richness (Chao index: 107-547) exhibited significant negative correlations with salinity, potentially associated with ionic stress from Na+, Cl-, and CO32-. Canonical correspondence analysis demonstrated that salinity, CO32-, total phosphorus, and Ca2+ collectively explained 68.26% of community variation. These findings highlight the susceptibility of fungal communities to the combined effects of ionic and nutrient stressors in shrinking plateau lakes, emphasizing the urgency of monitoring salinity-nutrient interactions to conserve ecological functions in fragile semi-arid aquatic ecosystems.