Grafted cucumber plants were grown in a new hydroponic system (“Kappa Land”, Mitsubishi Chemical Aqua Solutions, Co., Ltd., Tokyo, Japan). Two different nutrient management methods were applied to the plants as treatments: Electrical Conductivity-based Management (ECM) and Quantitative Nutrient Management (QNM). During the growth period, we examined plant growth characteristics and productivity, fruit growth characteristics and quality, and nutrient use characteristics. The results revealed that the QNM technique significantly reduced the nutrient supply rate per plant for Ca2+, SO42−, and N by 28.5%, 25.5%, and 23.3%, respectively. Similarly, the absorption rates per plant of SO42−, K+, and PO43− were reduced by 17.8%, 11.9%, and 10.9%, respectively. However, N, Ca2+, and Mg2+ absorption rates slightly increased in the QNM treatment. The nutrient wastes generated per kilogram of produced fruits were also reduced by 66.4%, 60.7%, and 30.2% for N, Ca2+, and SO42−, respectively. Although the QNM technique reduced the plant’s leaf area, it significantly increased its total length by 9.4%. The total and marketable yields were not significantly different between the ECM (9.0 and 8.0 kg plant−1) and QNM (9.1 and 8.2 kg plant−1) treatments. However, the QNM treatment produced the highest total dry matter of 617 g plant−1, surpassing the ECM treatment by 6.9%. On the other hand, differences in nutrient management methods did not significantly affect fruit quality, including total soluble solids, water content, skin color, size, and shape. These results suggest that with the QNM method, it is possible to produce quality cucumbers with high nutrient use efficiency while protecting the environment from nutrient wastes.