Terrestrial inputs-induced eutrophication in the P-depleted Northeastern (NE) Mediterranean shelf waters has led to changes in particulate organic matter (POM) composition and distributions in the water column and surface sediments. The present study aimed to understand the impacts of terrestrial nutrient and POM inputs on coastal eutrophication, bulk POM composition and concentrations in surface waters and sediments of the Mersin Bay, located at the Cilician Basin of NE Mediterranean Sea. The present results showed that the regional rivers and wastewater discharges markedly increased nutrient concentrations, leading to enhanced eutrophication and POM concentrations surface waters of the Mersin inner bay. The C/N and C/P molar ratios derived from the regressions of POM data in surface waters were 6.92 and 129, respectively. The higher C/N and C/P molar ratios in the surface sediments of productive Mersin Bay indicated selective decay of N, P-containing organic matter buried in muddy sediments. Close positive correlations were found in sediment organic matter and mud contents, indicating the crucial role of fine particles in transport and enrichment of organic matter in the muddy shelf sediments of NE Mediterranean Sea.