This chapter explores the application of disinfection technologies in indoor hydroponic systems, which are critical for mitigating pathogen risks and ensuring sustainable, safe crop production. Hydroponic cultivation, though advantageous in many ways, presents unique challenges due to the potential for pathogens like Salmonella, Fusarium to proliferate and circulate through nutrient solutions. To address these issues, various disinfection techniques are discussed, categorized into physical, chemical, and biological methods, as well as advanced oxidation processes (AOPs). Techniques such as UV radiation, hypochlorite treatment, and bacteriophage application are analyzed for their effectiveness, impact on crop quality, and environmental implications. The chapter emphasizes the importance of optimizing disinfection strategies to balance pathogen eradication with maintaining crop productivity and safety, paving the way for advancements in hydroponic farming technology.