The Nhecolandia is a sub-region of the Brazilian Pantanal wetland, where saline and freshwater lakes coexist in close proximity. Measurements of dissolved organic carbon (DOC) content and analysis of fluorescence excitation-emission matrices (EEM) were conducted in an effort to characterize spatial variability in concentration and source of dissolved organic matter (DOM) and to further understand the hydrochemical functioning of this complex environment. Increasing pH under the influence of evaporation resulted in an increasing DOC solubility ranging from 50 to over 300 mgC L-1 in surface water. Spectrofluorescence characterisation indicates the presence of several families of dissolved organic matter (fulvic and humic-type and proteinaceous materials), which are related to the type of lake and its hydro-bio-geochemical functioning. Moreover, the fluorescence signatures from lake water DOM and from surrounding soil-water-extracted organic matter (WEOM) show strong similarities although some labile proteinaceous compounds disappeared during humification. Results from the characterisation of DOM and WEOM not only suggest that spectrofluorescence is a reliable technique for the tracing of water flows, but also for the marking of the origin of organic horizons in this environment.