Despite their high ecological value, transboundary Mediterranean rivers and their coastal wetlands are subject to increasing anthropogenic stressors (intensive agriculture, industrial activities, population density) and are predicted to be particularly vulnerable to future climate change. Improving understanding of elemental cycling in these systems is critical for understanding these ecosystems' functioning and response to future pressures. Here we studied dissolved organic matter (C, N and P) cycling in the Evros/Марица/Meriç River, one of the most heavily polluted and, simultaneously, most ecologically valuable transboundary river systems in the Eastern Mediterranean. Measurements were performed in different seasons over a year (April 2009, July 2009, September 2009, April 2010 and July 2010 and along transects extending more than 70 km from the freshwater end-member to 2-km offshore in the Aegean Sea. Dissolved organic carbon (DOC) in Evros waters (DOC: 119 -496 μmol/L) was comparable to that of other large Mediterranean rivers (Rhone, Po). The organic component of N and P showed increased variability and ranged from 0.65 to 56 μmol/L for DON and from 0.03 to 4.15 μmol/L for DOP. In the lower parts of the river, where all point and nonpoint inputs converge, the high inorganic N inputs favored elevated assimilation rates by phytoplankton, and resulted in increased chl-a concentrations (up to 488μg/L) and autochthonous dissolved organic matter (DOM) production under dry conditions and low flushing rates. Moreover, the distribution of carbohydrates revealed a constant background of soil-derived mono-saccharides, and additional contributions of poly-saccharides during phytoplankton bloom events. During the dry season, inorganic nutrients and DOM from upstream sources remained restricted in the lower parts of the river (delta and coastal wetlands), while during high flow conditions upstream DOM was flushed to the sea and organic nitrogen forms became an important component of TDN (at least 40%) in the coastal and shelf waters. The co-existence of terrigenous material with autochthonous production and some anthropogenic contributions is supported by the large variability found in DOC:DON (4 -96) and DOC:DOP (79 ->1000) ratios, the positive correlation of DOC vs chl-a (r 2 = 0.76, p=0.01 for July 2009; r 2 =0.77 p=0.01 for September 2009), the decoupling between DOC and DON, and the observed spatial distribution of inorganic N forms including ammonium. Our results illustrate the combined and complex influences of (i) seasonally dependent hydrological processes, (ii) consistent upstream anthropogenic pollution sources, and (iii) irregular water resource management practices on C, N, P dynamics along this heavily polluted transboundary river system, its delta and wetland ecosystem, and adjacent Mediterranean coastal waters.