The global demand for medicinal plants is rapidly increasing, prompting the exploration of innovative cultivation techniques. Hydroponics, in particular, offers a promising method for producing high-quality medicinal herbs. This study was carried out as a factorial experiment using a completely randomized design with three replications, conducted in a research greenhouse in Zanjan, Iran. The experiment involved two basil genotypes (green and purple) and ten different growth media: cocopeat, perlite, sand, pumice, cocopeat + perlite (1:1), cocopeat + pumice (1:1), cocopeat + sand (1:1), pumice + sand (1:1), pumice + perlite (1:1), and sand + perlite (1:1), all under a hydroponic system. The results revealed that chlorophyll and carotenoid contents in both basil genotypes were significantly higher in the cocopeat + perlite and cocopeat + pumice media. In contrast, plants grown in sand and pumice substrates exhibited lower concentrations of photosynthetic pigments. Additionally, phytochemical parameters, including total phenols, flavonoid and anthocyanin content, antioxidant activity (measured via DPPH and FRAP assays), total protein, and PAL enzyme activity, were notably enhanced in the combined growth media, especially in the cocopeat + perlite medium. Conversely, the lowest values for these phytochemical traits were observed in plants grown in inorganic substrates, such as sand and pumice, either alone or in combination. Overall, the cocopeat + perlite medium was the most effective at improving both physiological and phytochemical parameters. In conclusion, optimizing growth media in hydroponic systems can significantly enhance the production of high-quality vegetables and medicinal herbs with superior nutritional value.