Heavy metals (Al, Fe, As, Cd, Cr, Cu, Hg, Mn, Ni, Pb, Zn) content was evaluated in suspended particulate matter and sediment samples collected from Vlora Bay (Albania) in the framework of Centro Internazionale di Scienze del Mare (CISM) Project activities. The trend of the metals (in general, overlapping that showed by the suspended particulate matter distribution), together with the linear correlation values found between metals, suggested the pivotal role of the Vjosa River and of the inner circulation scheme of Vlora Bay on their distribution. The geoaccumulation index, Igeo, was calculated as a criterion to assess if a metal concentration found in the sediment represents contamination level or can be considered as background level. The results show that metals concentrations in sediments can be considered near the background levels found in the Mediterranean Sea, even if some accumulation was found in several stations. The data were compared to Sediment Quality Guidelines considering the ERL (effects range low) and ERM (effects range medium) values, to evaluate the potential effects of sediment-associated metals on aquatic organisms. The Ni value for all samples was above the ERM value, while Cr and As values were in between ERL and ERM. Metal speciation was also evaluated in some sediment samples. Generally, the metals found were associated with the refractory phases, which constitute up to 80% of the total concentration. Moreover, the sampling strategies and the adopted analytical methods were compared to those recommended by national and international regulations.