In arid regions, excessive water use threatens agricultural sustainability and overall livelihoods. It is essential to minimize water consumption to address these issues. Date palm ( Phoenix dactylifera L.) is an emblematic crop of arid regions and a major water consumer. Tailoring current irrigation systems into new, water-efficient systems could help cope with the water consumption of this crop. Microbial communities associated with plants are essential for agricultural sustainability and could improve the water use efficiency in regions threatened by water scarcity. These communities should thus be seriously taken into account when adapting agrosystems to the current global change setting. However, no information is presently available on the effects of these modifications on date palm microbial communities. This study highlights the impact of different soil water systems (flooding and drip irrigation, natural conditions and abandoned farms) on date palm root fungal communities at different soil depths. The findings revealed that the soil water systems had a marked impact on fungal communities and that drip irrigation reduced the fungal diversity but increased the abundance of arbuscular mycorrhizal fungi. We showed that these effects were similar at all sampling depths. Finally, as the root architecture is a major determinant of water uptake, we reveal different behaviors of the root architecture under these different soil water systems to 160 cm depth. The findings of this study give new insights into the date palm root architecture and associated fungal communities, particularly in the context of the water availability crisis, which drives the adaptation of agricultural systems.