In order to characterize microfiltration foulants from natural waters, 12 isolated fractions from three natural waters were analyzed in this study. Hydrophobicity, molecular size distribution and fluorescence excitation-emission matrix (EEM) spectral parameters were employed in characterizing membrane foulants. It was found that natural water which contained more large molecules (> 10 kDa) in neutral hydrophilic (N-HPI) fraction could lead to greater flux reduction. However, hydrophobicity and molecular size distribution cannot be analyzed separately in respect of flux decline. Comparatively, fluorescence EEM spectroscopy is better at characterizing foulants because it combined both hydrophobicity and molecular size characters in the spectral parameters. It was found that the most fouling fraction could have a very special fluorescent region between 350 nm < Em < 400 nm and 220 nm < Ex < 250 nm (Em: emission wavelength; Ex: excitation wavelength). The subtraction of fluorescence EEM spectra between feed water and permeate water confirmed that most of the retained foulants came from this region. The proportion of fluorescence intensity in the special region could be a quantitative indicator for the prediction of MF fouling potential. (C) 2011 Elsevier B.V. All rights reserved.