Deciphering molecular structures of dissolved organic matter (DOM) components is key to understanding the formation and transformation of this globally important carbon pool in aquatic environments. Such a task depends on the integrated use of complementary analytical techniques. We characterize the molecular structure of natural DOM using an ion mobility quadrupole time of flight liquid chromatography mass spectrometer (IM Q-TOF LC/MS), which provides multidimensional structural information on DOM molecules. Geometric conformation of DOM molecules is introduced into molecular-level analysis via the ion mobility (IM) in the system, and an actual measurement of isomers is achieved for the first time. Our data show that natural DOM molecules from several south Texas rivers and adjacent coastal waters have smaller geometric conformation compared with standard biomolecules. Furthermore, about 10% of all DOM molecules resolved within the detection limit of IM-MS had at least one but no more than four isomers. With acquired geometric and isomeric information, we established a multidimensional database containing 89 natural DOM compounds. This database provides a foundation to expand further, or compare, with DOM data from different seasons and locations.