The complexity and variability of processes determining dissolved organic matter (DOM) quality is likely to increase in highly dynamic systems such as Mediterranean water bodies. We studied the dynamics of DOM in a Mediterranean lagoon dominated by seasonal submerged vegetation and receiving torrential freshwater inputs. In order to trace changes in DOM quality throughout the year in relation with potential DOM sources, we used spectroscopic techniques including UV-visible absorbance and fluorescence excitation-emission matrices. The quality of the lagoon DOM fluctuates on a seasonal basis between the characteristics of torrential inputs and macrophytes. Humification and aromaticity of DOM increased markedly after the torrential inputs of materials derived from terrestrial vegetation and soils in the catchment. The macrophytes in the lagoon contributed with less humified materials and protein-like compounds. Other minor processes such as seawater entrances, photodegradation or temporary bottom hypoxia translated into sporadic DOM quality changes. These results highlight the need of a whole ecosystem approach to understand changes in DOM quality due to ecosystem processes that might otherwise be exclusively attributed to DOM reactivity. © 2014 Springer International Publishing Switzerland.

This study was funded by the project CGL 2008-05095/BOS, from the Ministerio de Ciencia e Innovación (Spain). NC held a doctoral fellowship (FI 2010–2013) from the Generalitat de Catalunya and is currently sustained by the unemployment allowance of the Spanish Public Employment Service (SEPE).

Peer reviewed