Water serves as an essential resource for irrigation worldwide. The Agra Canal plays a vital role in the irrigation infrastructure of the Faridabad and Palwal districts in Haryana. India. An experimental setup was employed to assess the impact of canal water on locally grown vegetables (Spinach, radish, and tomato). The plants in each pot were irrigated using three different water ratios: 100% groundwater, 50% groundwater + 50% canal water mixing, and 100% canal water. After harvesting, rhizospheric soil was analyzed for similar parameters, followed by fungi characterization and DNA sequencing. Results indicated that location S2 had the highest microbial load, whereas location S6 had the lowest amount detected. It was observed that pots irrigated with 100% canal water exhibited higher microbial load compared to those receiving other watering ratios; this suggests that Agra Canal water contains a substantial amount of fungus, which negatively impacts crop yield, including Albifimbria verrucaria, Aspergillus novafumigatus, Aspergillus niger, Fusarium equiseti, Altenaria Spp., Chetomeaceae Spp., Humicola Spp., and uncultured fungal stains, have also been identified as dominating in rhizospheres soil, as well as in Agra canal water, indicating potential detrimental effects on plant health. In addition, to further explore potential risks, it is necessary to examine and reduce the sewage effluent discharge into Agra Canal.