Saline groundwater irrigation is a predominant practice, especially in date palm (Phoenix dactylifera L.) farms in arid agroecosystems with scarce freshwater resources. Despite its economic importance, the influence of saline groundwater irrigation on bulk soil fungi remains overlooked. This study examined how saline groundwater irrigation affects fungal diversity, community structure, and assembly processes. Bulk soils from date palm farms with distinct irrigation sources (freshwater and saline groundwater), were analysed, and fungal community analyses were done using the internal transcribed spacer 2 (ITS2) sequencing. Soils irrigated with saline groundwater had a lower percentage (27%) of unique operational taxonomic units (OTUs) compared to freshwater (33.3%). Fungal richness negatively correlated with soil pH. Differences observed in overall and guildspecific fungal communities, with irrigation water electrical conductivity (EC) emerging as a pivotal factor distinguishing between the two irrigation sources. Notably, pathotrophs abundance was significant in soils irrigated with saline groundwater. Furthermore, the dominant pathotroph Fusarium, exhibited drift-based assembly process and was observed to be high under saline groundwater irrigation. Our study reveals that groundwater salinity reduces the number of unique OTUs and alters fungal communities at the overall and guild levels. This insight aids agricultural improvement in regions where saline groundwater is a predominant water source.