Dissolved organic matter (DOM) in aquatic systems originates from a range of sources. Some is allochthonous, transported from the surrounding landscape to the water body, and is derived from and influenced by the geology, land use and hydrology of its origin. Some is created in situ through microbial activity, which may provide an independent source of organic matter, or a recycling mechanism for that which has been transported into the water body. The relative contribution of each source depends upon the location and environmental conditions within and without the water body. Human activity is also a source of DOM, much of which is believed to be labile, which can enter the aquatic system through direct point discharges, diffuse leaching and aerial dispersal. Fluorescence spectroscopy can provide an excellent tool to source DOM fractions, and to monitor and understand DOM transformations in aquatic systems, as much DOM has an intrinsic fluorescence. In particular, recent advances in optical technology, enabling rapid investigation of shorter wavelengths, have enabled more detailed characterization of organic material and its reactions in water. In this article, we review the use of fluorescence spectroscopic techniques to measure the intrinsic fluorescence of organic matter and the application of fluorescent DOM analysis in marine waters, freshwaters and wastewaters. Copyright © 2007 John Wiley & Sons, Ltd.