To investigate the extent of aluminum toxicity tolerance of eco-friendly, fast-growing, fresh water, pteridophytic Azolla-Anabaena symbiotic association in terms of altered physiological signals; Azolla microphylla Kaulf was exposed to 0 (control), 100, 250, 500, and 750 μM AlCl3, at pH 4.5 for 6 days. The adversity of Al was increased in a dose-dependent manner and the highest was recorded at 750 μM AlCl3. Despite the significant loss in membrane integrity (80% electrolyte leakage) due to an enhanced generation of H2O2, A. microphylla reflected only 50% growth inhibition (fresh and dry weight) at 500 μM AlCl3 (LD50). However, the average root length of Azolla was drastically reduced at high concentration due to their direct contact with aluminum-containing growth medium. Contrary to this, the whole association maintained moderate chlorophyll, carbohydrate content, photosynthetic efficiency, nitrogen-fixing ability, and nitrogen content at high Al concentration. Probably, growth protection was pertained through significant detoxification of H2O2 by employing an efficient antioxidative defense system including antioxidative enzymes (SOD, APX, and CAT) and non-enzymatic antioxidant carotenoids. An enhanced level of phenolics and flavonoids in the root exudates possibly maintained a non-toxic level of aluminum inside the cell (195.8 μg Al/g FW) which makes A. microphylla a suitable pteridophytic plant to not only remove toxic Al from the contaminated sites but also to improve nitrogen status of those regions. Graphical abstract ᅟ.