This study was conducted over a 6-month period (2018-2019) to study the inherent fungal contaminants of irrigation water in Al-Kharj farms. Water samples were collected from three sites of the wells (the north and south sides and the plastic housing) at the farms. Sewage samples were also collected. One hundred and sixty-seven fungal isolates were obtained from the wells and the sewage. These isolates belonged to 16 genera, of which 13 were deuteromycetes, one was a zygomycetes and one was an oomycete. The results showed that Pythium, Aspergillus, Rhizoctonia, Rhizopus, and Fusarium genera were found throughout most months of the year. The results for each month were similar in terms of the frequency of fungi detected (99.96–100%) and the fungi isolation frequency (average, 6.247–6.25%). Pythium, Aspergillus, Rhizoctonia, Penicillium, and Diplococcium were identified in the water samples taken from the wells and the plastic housing. Alternaria and Fusarium were identified in water samples taken from the wells, while Candida and Macrophoma were also found in water samples taken from the well, while Cladosporium was found in the water samples and the sewage samples. Rhizopus was found in water samples taken from all of the wells near the plastic housing. Ulocladium was found in water samples taken from the wells and the plastic housing, while Thielaviopsis was found in water samples taken from the wells near the housing and the sterile fungus was found in water samples taken from the wells and the plastic housing. Moreover, we found that the seed trap method was the best method for fungi isolation (isolation frequency, 11.17%) and was better than the direct method of isolation (isolation frequency, 8.53%).