In this study, the potential of Azolla filiculoides, a freshwater fern species, on phenanthrene phytoremediation and biodegradation was investigated. Furthermore, the effect of phenanthrene on growth performance, photosynthetic activity and biosynthesis, and accumulation of secondary metabolites of A. filiculodes were evaluated. Plants were grown in a nitrogen-free Hoagland and exposed to different phenanthrene concentrations (0, 1, 5, and 10 mg/L). Exposure to 10 mg/L phenanthrene caused a significant reduction (42%) in Azolla filiculoides growth compared to control on day 14. The photosynthetic pigment content of A. filiculoides treated with 1 and 5 mg/L was almost the same as the control, while 10 mg/L phenanthrene was significantly reduced. In comparison to unplanted controls, the biodegradation percentages obtained from the planted growth medium were found to be 88, 69, and 60%, respectively, for the application of 1, 5, and 10 mg/L phenanthrene. Data on plant growth, photosynthetic pigments, secondary metabolite contents, and biodegradation percentages indicated the tolerance level and the effective phytoremediation potential of A. filiculoides for phenanthrene was A. filiculoides is highly effective in phytoremediation of low concentrations of phenanthrene pollution in a short time.