Dissolved organic nitrogen (DON) is recognized as an important nitrogen (N) pool in soil N cycling, but its role in the N cycling of paddy soils, which are intensively fertilized, is not fully predicted. In this study, we investigated DON in flooded layer and soil solution along soil profiles with suction cups in fertilized paddy fields. The DON concentration showed a relative decrease in the deeper layer of paddy soil, while free amino acid N (FAA-N) exhibited a drastic increase along with nutrient profiles of soil. In the upper layer (0–20 cm), DON accounted for 54–64% of total dissolved N (TDN), but this value increased up to 63–97% in the deeper layer (40–60 cm). Low concentrations (9.6–15.0 μg L−1) of FAA-N and low percentage of FAA-N/DON (0.1–0.2%) were observed in the upper layer, but higher concentrations (111–307 μg L−1) and increased percentage (8–36%) were examined in the deeper layer. The high percentage of DON/TDN indicated that DON was the predominant N pool in the deeper layer. Concentrations of DON were significantly and positively correlated with organic matter, total N, and electrical conductivity (EC), while negatively related to soil pH. Additionally, capillary porosity, air porosity, bulk density and particle density were also found to be significantly associated with DON. We suggest the DON and FAA in the paddy field could be an important source for N leaching, which is most strongly related with soil nutrient profiles and physical properties. It is estimated that a total loss of 4.0 kg N ha−1 yr−1 is potentially linked to DON in the paddy field, which implied that ca. 3.35% of the applied N fertilizers could be lost via DON.