Because of Egypt's water scarcity, employing agricultural drainage water for fish farming presents significant challenges. Therefore, this research aims to compare the biochemical and histopathological parameters of the muscles of tilapia, Oreochromis niloticus, grown on a fish farm in Abassa, Abo-Hamad, Alsharkia, Egypt as a reference group and an aquaponic system built in the Faculty of Science, Tanta University, Egypt. In this study, 10 fish were collected from the fish farm in Abassa and 10 fish were collected from the aquaponic system. Thiobarbituric acid reactive substances (TBARS) and reduced glutathione (GSH) concentrations were evaluated in the muscles of fish collected from the reference site and aquaponic. Additionally, glutathione peroxidase (GPx), glutathione-S-transferase (GST), and catalase (CAT) activities in the muscle tissues of fish harvested from the fish farm and aquaponic system were assessed. Moreover, the histopathological changes in the muscles of the reference and aquaponic fish muscles were analyzed. The results showed a non-significant change (p > 0.05) in muscle TBARS level and GST and CAT activities in the aquaponic group in comparison with the reference group, respectively. However, there was a significant increase (p < 0.05) in muscle GSH level and GPx activity in the aquaponic group when compared with the reference group, respectively. The histopathological investigations showed some abnormal structures in the muscle tissues of the reference group, while it showed a normal muscle structure in the aquaponic group. In conclusion, this study proves that aquaponic systems can be used as a safe alternative for fish production.