Climate change, population expansion, water shortages, soil erosion, and food security are some of the primary concerns facing the world today. Hydroponic, aquaponic, and aquaculture systems may help to address these difficulties. Hydroponics is a closed-loop system for growing plants in nutrient-rich water rather than soil. Aquaponic systems combine hydroponics and the growing of fish or other aquaculture species in addition to plants. This review aims to evaluate the challenges encountered by aquaponic and aquaculture farming operations and identify which issues still need to be addressed. The review is organized as follows: recent previous studies on hydroponics, aquaponics, and aquaculture were collected and investigated; water quality and energy issues were addressed; technologies to improve water quality in these systems were discussed; and challenges to the implementation of large-scale aquaponics were discussed. The study found that a commercial reverse osmosis filtering system that provides excellent water quality control is a good method for removing harmful contaminants from water in small-scale aquaponics and aquaculture. Recirculation systems are more sustainable and effective in managing the volume of effluent in aquaculture units because only 10% of the total volume of water is refilled daily. Constructed wetland systems are a low-cost, high-efficiency treatment solution for nitrogen-containing wastewater, with removal efficiencies of up to 98% for NH4-N and above 98% for NO2-N. The use of aquaponics in desert settings with water constraints constraint is viewed as a possible sustainable food production approach.