Dissolved organic matter from natural waters is a complex mixture of various chemical components, which play vital roles in many environmental processes such as the global carbon cycle and the fate of many key anthropogenic pollutants. Despite its environmental significance, dissolved organic matter in natural form has never been studied using nuclear magnetic resonance based hydrodynamic radius measurements due to its extremely low concentration (e.g., a few mg/L) in natural waters. In this study, NMR-based hydrodynamic radius measurements were performed directly on unconcentrated pond, river, and sea waters. The key chemical components of the dissolved organic matters from different sources were identified as carbohydrates, carboxyl-rich alicyclic molecules, and aliphatic molecules. By using the Stokes-Einstein-Sutherland equation, the average hydrodynamic radii of the three key components were calculated.