The environmental status of the marine environment in the NE Adriatic Sea was assessed, using as a bioindicator species the Mediterranean mussel Mytilus galloprovincialis Lamarck, 1819. Samples were collected seasonally from mariculture sites and from major Istrian ports between the years 2010 and 2013. The condition indices of mussels ranged from 13.3 to 20.9% at mariculture sites and from 14.3 to 23.3% at port locations. The seasonally δC values of seawater varied between -10.9 to 0.7‰. Pollution by sewage sludge (based on δN values) was confirmed only in two ports. Tissue concentrations of Mn, Co, Ni, Cu, Zn, Se, Cd, and Pb were significantly higher in the tissue of the mussels collected from the ports (polluted sites). Arsenobetaine was the major As compound present in the samples and there was no significant difference in the levels of total As in mussel tissues from mariculture and port sites.