Dissolved organic nitrogen (DON) in aquatic systems is an important component of the global nitrogen cycle. However, the molecular structural information of DON in natural water is still unknown. In this study, the molecular structural characteristics of DON molecules in three natural waters were studied by using negative and positive ion mode electrospray ionization (ESI) Orbitrap mass spectrometry and collision-induced dissociation (CID). The DON compounds in these natural water samples could be selectively ionized by a positive ESI source with formic acid as the ionization promoter. A fraction of DON may exist as amphoteric substance. Then, possible chemical structures were assigned for some of these DON molecules by CID. Possible O-containing functional groups could be assigned as carboxyl, hydroxyl, carbonyl and methoxyl in negative/positive ESI tandem mass spectra, and neutral loss of NH3 corresponding to amino groups was observed for the first time in a positive ESI CID MSMS analysis, which demonstrated that a fraction of DON in natural water may exist as amino acid-like compounds. The results demonstrate that the positive/negative ESI CID Orbitrap MSMS method could provide valuable molecular structure information on DON in natural water.