This work investigated the effectiveness of marimo in restoring lake ecosystems, with a focus on its capacity for adaptive denitrification. Observations revealed a significant increase in granule size, benefiting its settling capability and thereby facilitating substantial reductions in nitrate levels and overall lake water purification. Notably, nitrate nitrogen was identified as pivotal in the nitrogen cycle, exhibiting a strong coupling relationship with denitrification processes. Marimo autonomously adjusted its denitrification in response to environmental nitrate levels, enhancing its nitrogen removal efficiency. Furthermore, Rhodobacteraceae was found to play an important role in nitrogen metabolism, with competitive interactions between Proteobacteria and Bacteroidota, influencing the overall efficiency of nitrogen removal. It was found that at first, the accumulation of nitrate enhanced denitrification, while afterwards, the decrease in nitrate concentration weakened denitrification. In addition, assimilatory nitrate reduction showed an upward trend throughout the entire process. Analysis of metabolic pathways further supported the adaptive denitrification adjustment mechanism of marimo. These findings highlight the potential of marimo as a natural solution for water quality improvement in lake ecosystems.