This study aims to monitor element-specific nutrient information during hydroponic cultivation by IoT-interfaced miniaturized ion sensors. Because of size, cost, and manufacturing advantages, solid-contact ion-selective electrodes (SCISEs) were fabricated as an ion sensor array and interfaced with wireless embedded-systems to construct an IoT nutrient sensor system (IoNSS) for the first time. The entire IoNSS framework was composed of (i) a nutrient solution sampling and sensing module with SCISEs controlled by an Arduino Due® microcontroller, (ii) a Wio Terminal® microcontroller for automated procedure setting, data recording, and wireless transmission, (iii) a private cloud server (a Network Attached Storage equipped with Node-RED® and MongoDB®) for data management, and (iv) MQTT webpage-based interactive interfaces. In experiments, we found that potentiometric signal resolution and noise of the Arduino-interfaced SCISEs were significantly improved and approached to instrumental DAQ-like quality by additional delta-sigma ADC (ADS1115®) chip conditioning. This facilitated cost-effective harvest of precise and high-quality IoT ion sensor data. Before on-site applications, each SCISE was two-point calibrated in multiple-ion solutions and was checked with the fixed interference method. The ion concentration measurements were also compared with those of commercial ISEs and ion chromatography. To test the system’s feasibility, the IoNSS was applied to cyber-monitoring of K+, NO3–, and NH4+ concentrations during two-week hydroponic cultivation of arugula (E. vesicaria) in an indoor plant factory (in Northern Taiwan) with a modified Cornell solution and an outdoor greenhouse (in Southern Taiwan) with a modified Yamasaki solution, respectively. It was demonstrated that the IoNSS was capable of real-time observation of the crop’s nitrate/ammonium utilization and nutrient solution’s EC-element dependency. Besides, the web interfaces successfully reported growing condition-dependent ion signals in a simultaneous and remote manner. To sum up, this work achieves novel cybermonitoring of element-specific nutrients by IoT-interfaced SCISEs and paves a promising way for intelligent hydroponic management.