Danshuei River Estuary (DRE) total and inorganic nitrogen in the dissolved (TDN, DIN) and particulate (TPN, PIN) phases were analyzed to study their distribution and partitioning. The carbon contents in particles were also analyzed. The upper estuary contained higher ammonium concentration (304–557 μM), leading to TDN completely dominating (>95%) the total N (TDN + TPN) pool within the DRE. Ammonium played a crucial role in controlling the speciation variation of DIN and partitioning between dissolved and particulate phases. Nitrification seemed to occur in the salinity >30 region where elevated percentages of nitrite and nitrate were observed. PON dominated the particulate N and contributed an average of 62% of the TPN pool. A constant organic C/N ratio (6.55) was observed in particles, indicating that POM was mainly from phytoplankton detritus. The N distribution coefficient values, log(K_D), ranged from 3 to 4, suggesting that the affinity of DIN for particles was weak.