The Azolla filiculoides plants were challenged with different arsenic (As) concentration under low pH stress conditions. The growth rate and doubling time of the plants were severely affected by higher As treatments at pH 5.00 when compared with stress pH 4.75 treatments. Hence, pH 5.00 was considered for further studies. In 10–30 μM As treated cultures, after 6 days, the relative growth rate (RGR) of Azolla plants was significantly reduced and in higher concentration of As, the RGR was negatively regulated. The root trait parameters were also significantly affected by increasing concentrations of As. Further, photosynthetic performance indicators also show significant decline with increasing As stress. Overall, the plants treated with 40 and 50 μM of As displayed stress phenotypes like negative RGR, reduced doubling time and root growth, browning of leaves and root withering. The total proline, H2O2, POD and Catalase activities were significantly affected by As treatments. Meantime, 30 μM of As treated cultures displayed 15 μg/g/Fw As accumulation and moderate growth rate. Thus, the Azolla plants are suitable for the phytoremediation of As (up to 30 μM concentration) in the aquatic environment under low pH conditions (5.00). Furthermore, the transcriptome studies on revealed that the importance of positively regulated transporters like ACR3, AceTr family, ABC transporter super family in As (10 μM) stress tolerance, uptake and accumulation. The transporters like CPA1, sugar transporters, PiT were highly down-regulated. Further, expression analysis showed that the MATE1, CIP31, HAC1 and ACR3 were highly altered during the As stress conditions.