Phytopigment concentrations (chlorophyll-a and phaeopigments), labile organic matter (proteins, carbohydrates and lipids), bacterial density and frequency of dividing cells were analysed in the sediments of a large coastal area covering the southern Adriatic continental shelf between Italy and Albania in order to describe the trophic status of coastal marine sediments. On average, sediments of the Italian coast displayed the highest phytopigment and biopolymeric carbon concentrations compared to sediments of the Albanian coast and indicated an increased nutritional status of this coastal ecosystem. Different trophic conditions were evidenced in terms of biopolymeric composition of sedimentary organic matter as an increase in protein and a decrease in the carbohydrate contributions to total biopolymeric carbon was observed moving from the Albanian to the Italian coast. Using a benthic approach for the evaluation of trophic status shallow Italian sediments (0–50 m) were mainly classified as eutrophic and were subjected to stronger anthropogenic disturbance. This was particularly evident in areas in front of city harbours (Brindisi and Barletta) that were classified as hypertrophic and displayed the highest biopolymeric carbon (BPC) concentrations and protein to carbohydrate ratio (PRT:CHO on average >1). In contrast Albanian sediments as well as deeper Italian stations (>50 m), resulted mainly in meso-oligotrophic and displayed lower BPC and PRT:CHO ratio (on average <1). The study of bacterial variables provided an improved approach for the conceptual definition of trophic state using benthic biochemical measures. An inverse relationship occurred between the nutritional contents and the bacterial density within meso-oligotrophic sediments. This may reflect an increase in ecosystem organization and complexity (i.e. increased abundance of the higher trophic levels) which may determine a reduction of the bacterial density at increasing trophic conditions. In contrast a positive correlation was found within eutrophic and hypertrophic sediments suggesting that at high organic matter concentrations the ecosystem is no longer capable of further organization.