Modern economic development of the Boka Kotorska Bay, known for its outstanding natural values, in terms of dynamics and size, is often not in line with the principles of environmental protection. As a consequence, over the recent decades, the Bay has been exposed to anthropogenic pollution. Marine sediment acts at the same time as a depositor and also the secondary source of pollutants, thus the analysis of pollutants in sediment is of vital importance for the estimation of its quality. Based on the results obtained over the past two decades, this paper considers characterization of sediment of the Boka Kotorska Bay in terms of heavy metal content and an assessment of heavy metal contamination in sediment and biota (Mytilus galloprovincialis and Posidonia oceanica), by applying environmental quality indexes: Enrichment Factor (EF), Metal Pollution Index (MPI), and Geo-accumulation Index (Igeo).