This study investigates the bioaccumulation factors (BAF) of total mercury (THg) in the liver, muscle, and gills of three commercially important fish species—Solea solea (Common sole), Dicentrarchus labrax (European seabass), and Mugil cephalus (Flathead mullet)—collected from the Adriatic Sea near the Ishëm River estuary, Albania. Mercury concentrations in fish tissues, as well as in water and sediment, were measured using Cold Vapor Atomic Absorption Spectroscopy (CVAAS; MA-2000 analyzer). BAF values were calculated relative to both water and sediment mercury concentrations. Among the three species, D. labrax exhibited the highest BAF for muscle relative to water (36.67), whereas S. solea had the highest BAF for liver relative to sediment (2.67). M. cephalus generally showed lower BAF values, consistent with its detritivorous feeding habits and lower trophic position. Significant interspecific and tissue-specific variations in BAF were observed, reflecting differences in feeding ecology, habitat use, and physiology. These findings underscore the value of BAF as an integrative metric for assessing bioavailability and trophic transfer of mercury in aquatic ecosystems and highlight the role of species-specific traits in modulating mercury accumulation.