The objective of our study was to provide a comprehensive evaluation on C, N, P cycling in medium sized Mediterranean rivers, such as the Evros, experiencing multiple pressures (intensive agriculture, industrial activities, population density). Our work aims also to contribute to the development of integrated management policies. Dissolved organic matter (DOM) cycling were investigated, during a one-year study. It was shown that the organic component of N and P was comparable to those of large Mediterranean rivers (Rhone, Po). In the lower parts of the river where all point and non-point inputs converge, the high inorganic N input favour elevated assimilation rates by phytoplankton and result in increased chl-a concentrations and autochthonous dissolved organic matter (DOM) production during the dry season with limited water flow. Moreover, carbohydrate distribution revealed that there is a constant background of soil derived mono-saccharides on top of which are superimposed impulses of poly-saccharides during blooms. During the dry season, inorganic nutrients and DOM are trapped in the lower parts of the river, whereas during high flow conditions DOM is flushed towards the sea and organic nitrogen forms can become an important TDN constituent (at least 40%) transported to shelf waters. The co-existence of terrigenous material with autochthonous and some anthropogenic is supported by the relatively low DOC:DON and DOC:DOP ratios, the positive correlation of DOC vs chl-a and the decoupling between DOC and DON. Overall, this study showed that in medium size Mediterranean rivers, such as the Evros, intensive agriculture and pollution sources in combination with water management practices and climatic variability are important factors determining C, N, P dynamics and export to coastal seas. Also, it highlights the importance of the organic fraction of N and P when considering management practices.