Greenhouse and aquaponic productions of basil (Ocimum basilicum L.) are well established, but the comparison between these two methods is not studied in detail. A study was conducted to evaluate the performance of basil in both aquaponic and soil systems under greenhouse conditions. The plants were raised in aquaponic beds with ornamental fish and a set of plants was raised in soil pots under a greenhouse setup. The studied parameters were morphological, biochemical and antioxidant levels. In order to analyze the stress effects of an aquaponic system on plant defense mechanism, two different antioxidant enzymes (catalase and peroxidase) were analyzed. Water quality parameters were monitored during the entire study period. Based on the results, there was a significant increase in growth parameters in the aquaponic system when compared to the conventional greenhouse cultivation of basil plants. The photosynthetic parameters showed a decline in the aquaponic system, but the biochemical parameters showed an enhancement in the aquaponic system of growing basil plants. The antioxidants exhibited a significant increase in the aquaponic system, which suggests a water stress effect on the plants induced by the aquaponic growing system. From the results of this study, it can be concluded that the aquaponic system is the best suitable method for basil production in the UAE condition.