Hydroponic cultivation is of considerable interest to the production of high-quality green plants. However, establishing the planting operating systems in hydroponic cultivation may result in chronic problems, such as the reproduction of harmful bacteria throughout the circulating culture fluid. Extensive research has been conducted on this type of cultivation using an ultraviolet sterilization system to prevent culture fluid contamination. In this study, the proposed module, using UV-C LEDs that emit wavelengths between 270 and 285 nm, was designed along with a sensor and controller. The module was set to emit 300, 500, and 700 mW, for different culture fluid flow rates, to investigate its capacity to eliminate Escherichia coli (E. coli), Clavibacter michiganensis (C. michiganensis), Pseudomonas cichorii (P. cichorii), and Fusarium oxysporum (F. oxysporum). Resultantly, the maximum flow rate of the culture fluid was verified for the complete sterilization of each harmful bacterium.