In recent years, controlled environment agriculture (CEA) has gained popularity as a sustainable and efficient method of cultivation, offering solutions to challenges posed by traditional farming practices and meeting the growing demand for high-quality produce. However, advancements in CEA have raised concerns about food safety, requiring new approaches to minimize the risk of produce contamination. This research explores the effectiveness of a bacteriophage cocktail as a biocontrol agent against Salmonella contamination in lettuce grown in water-recirculating systems. Salmonella Newport and Salmonella Typhimurium (103 CFU/mL) were inoculated into aquaponic and hydroponic nutrient solutions into a water-recirculating system to mimic sporadic contamination, followed by treatment with a bacteriophage cocktail (S7, S10, and S13) at different multiplicities of infection (MOI 0.01 and MOI 1). The results demonstrated a significant reduction in Salmonella Newport and Salmonella Typhimurium populations at both MOI 0.01 and MOI 1 in aquaponic and hydroponic nutrient solutions, with levels reaching below the limit of detection (LOD) after 3 to 4 days of bacteriophage cocktail inoculation. From the plant parts, there was a significant reduction in the microbial population of Salmonella serovars in media plugs and roots from the hydroponic nutrient solution, reaching levels below the LOD in both phage cocktail treatments after a 2-day inoculation period. Contrarily, significant reductions were not observed in Salmonella serovar levels in plant roots and media plugs from the aquaponic nutrient solution treatment. These findings highlight the potential of utilizing bacteriophages to improve food safety in indoor-grown lettuce by controlling Salmonella populations while also indicating the necessity for further research to understand the microbial dynamics within each type of system.