The data contains 12 sets of average diffusion coefficients and hydrodynamic radii of the major Dissolved Organic Matter (DOM) components in natural waters. The Bruker Avance 500 nuclear magnetic resonance (NMR) spectrometer was used to perform the ?H Pulsed Gradient Spin-Echo NMR diffusion experiments. The data is the product of the sample and the machine analysis. The data is organised using OriginPro8 software and (Bruker) TopSpin for the operating files from the spectrometer.