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Tomato is a vegetable crop commonly grown in Nigeria and consumed by most people. It contains vitamins and vital nutrients that are essential for good health. This study was conducted to determine the effect of magnetization of irrigation water on the growth, yield and nutritional qualities of tomatoes under deficit irrigation. Tomato seeds (‘Roma VF’ and ‘UC 82B’ varieties) were planted in 96 buckets (11 liters capacity), 48 buckets for magnetized water (MW) and 48 buckets for non-magnetized water (NMW), grown in a greenhouse and harvested 82 days after planting. The irrigation water was treated with 30 pieces of 10×25×50 mm neodymium magnets (1.2 Tesla). The tomato plants were subjected to deficit irrigation to determine the effect on the performance of tomatoes at 100% (1 liter), 80% (0.8 liters), 60% (0.60 liters) and 50% (0.50 liter) water requirement. Each treatment was replicated 6 times for both MW and NMW. The MW increased the growth of ‘Roma VF’ and ‘UC 82B’ varieties by 5.44-38.10% and the stem girth by 21.13-49.01%. MW increased the yield of ‘Roma VF’ variety by 110.00%, 36.00%, 6.26% and 24.00% for 100%, 80%, 60% and 50% of water application, respectively but increased the yield of ‘UC 82B’ variety by 56.52% for 100% water application. MW also improved vitamin A and C content by 7.89-27.94% and 0.45-19.06%, respectively. The concentrations of Lead were slightly higher in the tomato irrigated with MW than in the NMW but values of other heavy metals were not consistent and very close for both MW and NMW.