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Waterlogging is an acute problem in the agricultural areas of arid regions. This study highlights the main reasons for water table rise in the Wafra agriculture area of South Kuwait. A two-tier aquifer system exists in the area, which consists of the Kuwait Group aquifer underlain by a semi-confined Dammam aquifer. Improper sealing of wells tapping the semi-confined Dammam aquifer and over-irrigation were the main reasons for water level rise, and an increase in total dissolved solids was due to high evaporation of brackish water used for irrigation in the area. Other issues such as thin soil cover, topographic variation, and geomorphology within the area play an interactive role in the development of salt crusts on the ground surface. The key solution to the problem lies with proper well design and irrigation management. The sealing of the wells tapping the Dammam Formation has resulted in the lowering of the water level, which has allowed the reclamation of farms. For sustainable management of the Wafra agriculture area, it is observed that only the Kuwait Group aquifer should be utilized for irrigation, dewatering should be carried out in selective low-lying areas, and the adoption of best irrigation practices can be the only way for sustainable agriculture development in the area. The use of tertiary-treated wastewater, along with groundwater from the Kuwait Group (KG) aquifer, can be a solution to sustain agriculture. The crop water requirement should be considered for irrigation application while using best practices such as drip irrigation.