A vital goal of cleaner production involves developing agricultural production systems capable of ensuring sufficient yields of highly necessary foods to meet the increasing needs of the global population while minimizing the associated economic and ecological costs. Integrated agri-aquaculture systems (IAAS) offer a number of advantages for sustainable agriculture, including water reutilization, discharge mitigation, and increased profitability by leveraging the symbiotic relationship between organic waste, bacterial mineralization, and plant filtration. The aim of this study was to assess the production of two food items of global socio-economic importance cultivated at different salinities: Pacific white shrimp (Penaeus vannamei) and tomatoes (Solanum lycopersicum L.) grafted to salinity tolerant wild tomatoes. Pacific white shrimp were cultured at a density of 125 organisms/m3 and tomatoes at a density of 3 plants/m. The shrimp growth test consisted of three salinity levels: 2, 4, and 6 g/L. The corresponding tomato salinity treatments were conducted using shrimp water effluents; Steiner's universal nutrient solution (SNS) was used for the control treatment. The experimental period lasted 175 days. The highest tomato production (77.46 t/ha) was attained with SNS, with no significant difference from the salinity of 2 g/L. Shrimp final mean weight, survival, and production were higher at the 6 g/L salinity; and all the other zootechnical parameters decreased with lower salinity. When compared with the hydroponic system using a cost-benefit analysis (CBA), the production costs associated with the IAAS were lower primarily because of the reduced (or null) costs of fertilizer, and irrigation water. When grafted plants were used, the salinity tolerance of the commercial hybrid increased and shrimp could be cultured at appropriate salinity to facilitate osmoregulation. Chemical fertilization requirements were reduced and acceptable yields were obtained for the tomato crop by grafting to salinity-tolerant rootstocks.