Organic lettuce production in hydroponic systems often yields less than conventional production. A previous study from the lab found that organic nutrient film technique (NFT) system with Pre-Empt organic fertilizer contained high concentrations of nitrite ions, which likely induce stress and resulted in lower lettuce yield. To address this toxicity, we conducted a series of studies investigating the effect of reservoir aeration, with the hypothesis that aeration would enhance microbial mineralization of organic nitrogen and reduce the concentrations of phytotoxic compounds such as nitrite and ammonium. In the first study, we aerated NFT reservoir tanks with 15.9 mL/L (2 oz/gal) Pre-Empt organic fertilizer. Aeration increased dissolved oxygen (from 6.4 to 7.8 mg/L) and decreased the ratio of nitrite-nitrogen to nitrate-nitrogen (from 1.1 to 0.2) but did not affect ammonium. As a result, aeration increased yield of ‘Casey’ lettuce by 2.6 times. In the second study, aeration did not increase lettuce growth when the concentration of Pre-Empt fertilizer decreased to 10.6 mL/L (1.4 oz/gal). Furthermore, in the third study, we found cultivar-specific response to the aeration of organic fertilizer. These results suggested that aeration can enhance mineralization of organic nitrogen, reduce root-zone nitrite toxicity and increase lettuce yield at high fertilizer rates and potentially depending on cultivar.