The nitrogen removal performance of bioretention urgently needs to be improved, and sponge iron has great potential to address this challenge. This study reported the results of a long-term investigation on bioretention columns improved by sponge iron, examining the durability of sponge iron from nitrogen removal performance, sponge iron properties, and the evolution of biological elements. The results showed that after 9 months of continuous operation, the removal rates of ammonia nitrogen (NH4+-N), nitrate nitrogen (NO3--N), and total nitrogen (TN) in the bioretention columns with an appropriate proportion of sponge iron could reach 80% (some even over 90%). However, the long-term stress of sponge iron exposure, combined with the cumulative effect of pollutants, might lead to the excessive accumulation of reactive oxygen species (ROS) in plants, thereby posing risks of diminished chlorophyll content and enzyme activity. Simultaneously, the extended exposure could also have detrimental effects on microbial diversity and the abundance of dominant bacteria such as Proteobacteria and Sphingorhabdus. Therefore, it is necessary to select plant species and functional genes that demonstrate high adaptability to iron-induced stress.