The concentration of major and trace elements was determined for tomato (Lycopersicon esculentumcv. Aromata F1) fruits grown in three different substrate systems. The systems were soil and rockwool irrigated with a normal nutrient solution and rockwool irrigated with a nutrient solution with elevated electrical conductivity (EC). At three harvest times, tomato fruits were analyzed for Ca, Cu, Fe, K, Mg, Mn, Na, P, S, Sr, and Zn by ICP-AES and for Cd, Cr, Mo, Ni, Pb, Sn, and V by HR-ICPMS. The concentrations of Ca, Cd, Fe, Mn, Mo, Na, Ni, Sr, and Zn were significantly different (p < 0.05) for tomato fruits grown on the different substrates. Between the harvest times different levels (p < 0.05) were shown for Ca, Cd, Fe, Mn Na, Ni, Sr, Zn Cu, K, Mg, P, Sn, and V. The concentration of Cd was >15 times higher and the concentration of Ca was 50-115% higher in soil-grown fruits than in rockwool-grown fruits. Principal component analysis applied on each harvest split the data into two groups. One group includes soil-grown fruits, and the other group includes rockwool-grown fruits with the two different nutrient solutions.