This study examines mercury (Hg) bioaccumulation in the liver of three fish species—Solea solea (Common sole), Dicentrarchus labrax (European seabass), and Mugil cephalus (Flathead mullet)— from the Adriatic Sea near the Ishëm River Estuary in Durrës, Albania. It compares Hg levels across species and size groups, linking them to environmental Hg in water and sediments. A total of 252 fish were sampled, divided into small and large groups, and analyzed for liver Hg using Cold Vapor Atomic Absorption Spectrometry (CVAAS MA-2000). Water and sediment samples from the Ishëm River and Adriatic Sea were also assessed to evaluate Hg pollution. Hg concentrations in fish liver varied significantly among species. Dicentrarchus labrax displayed the highest levels, with averages of 12.6 µg/kg (large group) and 15.6 µg/kg (small group). Solea solea followed, averaging 14.5 µg/kg (large group) and 14.1 µg/kg (small group), while Mugil cephalus showed the lowest concentrations, with 5.9 µg/kg (large group) and 14.3 µg/kg (small group). Environmental Hg levels were higher in river water (2.83 µg/L) compared to seawater (0.42 µg/L), and riverine sediments (8.03 µg/kg) contained more Hg than marine sediments (5.4 µg/kg). Statistical analysis revealed a significant correlation (p < 0.05) between Hg levels in fish liver and water, highlighting the influence of environmental Hg on bioaccumulation. ANOVA results indicated significant differences in Hg accumulation across species and size groups (F = 2.911, p = 0.029), with Mugil cephalus exhibiting the most notable size-related variation (p = 0.047). The findings show Hg bioaccumulation in fish liver is influenced by species-specific traits, size-related factors, and environmental Hg availability. This study highlights the need for continuous monitoring of Hg levels in aquatic ecosystems to protect marine life and human health, along with targeted policies and mitigation strategies to address Hg pollution, especially in riverine and estuarine areas.