Hydroponics offers a promising approach to help alleviate pressure on food security for urban residents. It requires minimal space and uses less resources, but management can be complex. Microscale Smart Hydroponics (MSH) systems leverage IoT systems to simplify hydroponics management for home users. Previous work in nutrient management has produced systems that use expensive sensing methods or utilized lower cost methods at the expense of accuracy. This study presents a novel inexpensive nutrient management system for MSH applications that utilises a novel waterproofed, IoT spectroscopy sensor (AS7265x) in a transflective application. The sensor is submerged in a hydroponic solution to monitor the nutrients and MSH system predicts the of nutrients in the hydroponic solution and recommends an adjustment quantity in mL. A three-phase model building process was carried out resulting in significant MLR models for predicting the mL, with an R2 of 0.997. An experiment evaluated the system’s performance using the trained models with a 30-day grow of lettuce in a real-world setting, comparing the results of the management system to a control group. The sensor system successfully adjusted and maintained nutrient levels, resulting in plant growth that outperformed the control group. The results of the models in actual deployment showed a strong, significant correlation of 0.77 with the traditional method of measuring the electrical conductivity of nutrients. This novel nutrient management system has the potential to transform the way nutrients are monitored in hydroponics. By simplifying nutrient management, this system can encourage the adoption of hydroponics, contributing to food security and environmental sustainability.