The isolation, characterization and study of the properties of aquatic dissolved organic matter (DOM) still represent a challenge because of the heterogeneity, complexity and low concentration of organic material in natural waters. Based on its ability to interact with contaminants and thus to modify their transport and bioavailability, DOM is of interest for environmental purposes. The objective of this work was to better characterize DOM in the Gironde Estuary (southwestern France). The estuary represents an exchange zone between the continent and the Atlantic Ocean and conditions the transfer of organic and inorganic substances from the continental to the oceanic environment. Several samples were collected along the estuary during three cruises in 2002 and 2006. They were analysed using excitation-emission matrix (EEM) spectroscopy, a sensitive technique that allows direct analysis of water samples. Fluorescent DOM and dissolved organic carbon (DOC) did not behave conservatively in this estuarine system, i.e. the organic material did not undergo simple dilution from the upstream to the downstream part of the estuary. A seasonal variability in DOC content was pointed out, whereas few seasonal variations in DOM fluorescence were observed. DOM sources and processing in the estuary were further evaluated by determining two fluorescence indices - the humification index (HIX) and the index of recent autochthonous contribution (BIX). By applying these indices, the relative degree of humification (HIX) and autotrophic productivity (BIX) could be assessed. Based on the fluorescence and DOC results, the estuary was divided into three zones depending on salinity (S) and characterized by specific DOM: (i) A turbid zone of low salinity (S < 5) and high suspended particulate matter concentration with increase in the intensities of the α′ and α fluorophores, characteristic of humic-like compounds. (ii) A mid-estuarine zone (5 < S < 25) characterized by low autotrophic productivity and containing strongly degraded organic material, as shown by the low values of BIX and high values of HIX. (iii) A higher salinity area (S > 25) characterized by increased autotrophic productivity and a marked marine influence, and associated with high and low values of BIX and HIX, respectively. The HIX and BIX indices were shown as useful tools for readily defining and classifying DOM characteristics in estuarine waters.