The growing global demand for tuna has raised concerns over heavy metal contamination, as these apex predators can bioaccumulate toxic elements through the marine food web. Chronic exposure to lead (Pb), cadmium (Cd), and mercury (Hg) via seafood consumption poses potential public health risks, particularly for sensitive groups such as children and women of reproductive age. This study quantified Pb, Cd, and Hg concentrations in fresh and frozen yellowfin tuna (Thunnus albacares) over five years and evaluated non-carcinogenic risks using Target Hazard Quotient (THQ) and Total Target Hazard Quotient (TTHQ) metrics. Risk estimates were calculated for children (2–5 years and 6–11 years) and women under both average and high-consumption scenarios. Results indicated that Pb and Cd contributed minimally to overall risk, whereas Hg consistently dominated the THQ profile. For most scenarios, THQ and TTHQ values remained below the United States Environmental Protection Agency’s safety threshold of 1.0; however, exceedances were observed in some years for women with high consumption levels. Comparison with global datasets showed that heavy metal concentrations in Benoa Bay tuna were generally lower or comparable to those in other regions of concern, yet still within the worldwide range reported for tuna and other seafood products. These findings highlight the importance of continued monitoring, particularly in areas influenced by urbanization and industrial activities, alongside risk communication strategies and integration of seafood safety into national food policies. Such measures are critical to safeguard public health while advancing Sustainable Development Goal (SDG) 14.