In order to reduce excessive nitrate ion concentrations in vegetables, which may be one of the causes of high blood levels of methemoglobin, the effect of organic fertilizer on yield in hydroponics and the nitrate ion concentration in Japanese hornwort cultivated using the deep-flow technique was evaluated. To investigate seasonal variability, one series of experiments was conducted in three seasons, namely, spring, summer, and autumn. The nitrate ion concentration in Japanese hornwort decreased with the increasing proportion of organic fertilizer to total fertilizer applied; Japanese hornwort plants grown in culture medium containing both organic and chemical fertilizers were able to reduce the nitrate concentration compared with those grown in culture medium containing only chemical fertilizer. In spring and autumn, the nitrate concentration of Japanese hornwort grown in culture medium containing only organic fertilizer was the lowest, although plant height was the lowest. Additionally, when using hydroponics with Japanese hornwort cultured in medium containing only organic fertilizer, it was necessary to lower the temperature of the hydroponic solution to below25℃. These results suggest that a reduction in nitrate ion concentration, whilst maintaining the yield of hydroponically grown plants, is possible in Japanese hornwort when chemical fertilizer is used together with organic fertilizer.