Abstract: To investigate the temporal and spatial distribution characteristics of dissolved organic nitrogen（DON）concentration and urea（Urea-N）concentration and their effects on phytoplankton community structure in Xiamen waters, the surveys of dissolved organic nitrogen concentration, Urea-N concentration and phytoplankton communities were conducted in Xiamen waters in April（spring）and August（summer）of 2022. The temporal and spatial distribution characteristics and correlations of DON concentration, Urea-N concentration and phytoplankton communities were analyzed. The results were as follows: The DON concentration showed a trend of higher in the bay than outside the bay, and its average concentration was higher in spring than that in summer, with the highest concentration in West water. The average concentration of Urea-N was higher in summer than in spring, with a gradually decreasing trend from nearshore to offshore, and the highest concentration were found in the Jiu'long River estuary. The average abundance of phytoplankton in spring and summer is 8.4 × 10⁶ cells·L⁻¹ and 1.76 × 10⁶ cells·L⁻¹, respectively. The dominant species were Chaetoceros, Skeletonema costatum and Chaetoceros debilis in spring, with Skeletonema costatum Chaetoceros curvisetus and Rhizosolenia fragilissima in summer. The average abundance of phytoplankton, diatoms, and dinoflagellates showed the high value in Tong'an water and the West water during spring, with the high value in Southeastern waters during summer. The results of Correlation analysis were as follows: A significant negative relationship showed between DON concentration, Urea-N concentration and salinity, Dinoflagellates abundance; A significant positive correlation between phytoplankton abundance and temperature in spring. The research results show that the main sources of DON and Urea-N in Xiamen waters were from the runoff input from the Jiu'long River and the discharge input from land-based sources such as domestic sewage and industrial and agricultural wastewater. DON and Urea-N have important effects on phytoplankton community structure（especially dinoflagellates）in Xiamen waters.