In coastal ecosystems, the nitrogen fixation of seagrasses is crucial. However, the nitrogen fixation rates of seagrasses can vary spatially and temporally, especially in tropical regions. To investigate the nitrogen fixation rates of Enhalus acoroides, we used principal component analysis to examine the rates of nitrogen fixation in the roots, rhizome, and leaves of E. acoroides during the southwest monsoon (July) and the northeast season (October and January), respectively. The results showed that the nitrogen fixation rates in all three parts of E. acoroides were significantly higher during the southwest monsoon period compared to the northeast period. The rates of nitrogen fixation in the leaves of E. acoroides were found to be higher than in the roots and rhizomes. The difference in nitrogen fixation between the various parts of E. acoroides was highly significant (p<0.01). The nitrogen fixation activity of E. acoroides was significantly affected by temperature, as determined by principal component analysis. The spatial variations observed in different regions of E. acoroides were influenced by environmental factors in addition to the temperature-driven seasonal changes. The results suggest that temperature plays a vital role in the nitrogen fixation ability of E. acoroides.