Open hydroponic systems are the most widely used hydroponic systems in Korea. However, water drainage from the open hydroponics often causes significant environmental pollution due to agrochemicals and loss of water and nutrients. The objectives of this study were to show the potential application of an irrigation schedule based on threshold values of volumetric substrate water content tomato (Solanum lycopersicum L. ‘Betatini’) cultivation in a commercial hydroponic farm. This study was performed for minimizing effluent from coir substrate hydroponics using a frequency domain reflectometry (FDR) sensor-automated irrigation (FAI), as compared with conventional timer-irrigation (TIMER) from the farmer’s experience. The irrigation volume and retained water volume in the substrate of the TIMER during autumn to winter cultivation were 6.1-fold and 2-fold higher, respectively, than those of the FAI with slightly higher fruit weight and no difference in plant growth in the TIMER. This resulted in 1.9-fold higher water use efficiency (WUE) in the FAI. The irrigation volume and retained water volume in the substrate of TIMER during spring to summer were 3.2-fold and 1.8-fold higher, respectively, than those of the FAI with no difference in fruit weight or plant growth between the two treatments, which led to a 1.9-fold higher WUE in FAI. Approximately 61% fertilizer cost savings and a substantial decrease in drained solution volume were observed for FAI compared to those with TIMER. The use of the FAI technique for a least-drainage hydroponic system can be achieved in a large-scale hydroponic farm, resulting in efficient and environmentally sustainable use of water and fertilizer.