“Fertigation” is a distinctive system of fertilizer application. The roots of the plants are gathered in the soil under an irrigation drip. It is thought that the absorption of some nutrients that are affected by root growth in fertigation differs from a conventional fertilizing system. In this study, the effects of some nitrogen (N) sources in fertigation on tomatoes’ uptake of nutrients from the soil and fertilizer were examined and compared with conventional cultivation. The tomato yield was decreased by calcium nitrate (CN) fertigation in a phosphorus (P) deficient condition. In contrast, ammonium nitrate (AN) fertigation did not decrease the yield in a P deficient condition. The amount of P uptake in CN fertigation was less than in AN fertigation. AN fertigation also increased Ca and Mg uptake by the tomatoes because AN can be exchanged with the nutrients in the soil. The exchangeable calcium and magnesium contents of the soil under an irrigation drip after cultivation decreased in the AN fertigation treatment. There was no positive correlation between the amount of root and P uptake of tomatoes.