DOM has a vital role in the environmental fate of numerous contaminants including trace metals and organic compounds. The aim of this research is the spectroscopic characterization of the DOM of sediment samples collected from the shoreline of a coastal and heavily modified Mediterranean lake, the appraisal of DOM nature and origin, the evaluation of impacts from lithology and land uses, the comparison of the relative effectiveness of spectroscopic approaches for chemical classification and the final combination of the results provided from each approach. UV–Vis absorption spectra suggest the presence of low molecular weight and a photochemical bleaching of chromophoric DOM. Spectral slope ratio had a negative correlation with autochthonous production and DOM molecular weight. Fluorescence spectra showed that DOM is mainly freshly produced and has an autochthonous origin. Chromophores are of a rather simple structure deriving from the degradation of plant components. The contribution of submerged springs in organic matter input was uncovered. FT-IR spectroscopy revealed the presence of aliphatic and aromatic chains. The presence of carboxylic, phenolic, alcoholic and polysaccharide groups was supported. A correlation of recent autochthonous material with relative depletion in hydroxyl, carboxyl, alcoholic and polysaccharide groups was found. The morphological particularity of the area with its permeable lithology and the presence of karstic springs, in combination with the land uses of the catchment area hosting heavy industrial, agricultural and urban activities, in addition to the high archaeological and ecological importance of the wetland and its surrounding area, may require the application of a sound management and environmental protection scheme.