Coastal lagoons are highly enriched by heavy metals due to various natural and anthropogenic pressures. Sediment heavy metal pollution status and potential health risk assessment of the Akyatan Lagoon were determined from the seasonally obtained sediment samples between January 2022 and October 2022. The heavy metal concentrations in surface sediments of the Akyatan Lagoon ranged between 25.73 and 70.87 g/kg for Al, 10.28–31.03 mg/kg for Co, 0.11–1.42 mg/kg for Cd, 56.22–181.64 mg/kg for Cr, 10.06–34.16 mg/kg for Cu, 13.94–43.39 g/kg for Fe, 361.45–1118.82 mg/kg for Mn, 61.53–209.42 mg/kg for Ni, 9.46–34.43 mg/kg for Pb, and 19.57–117.42 mg/kg for Zn, respectively. The calculated ecological risk indices showed moderate Co, Cd, Cr, Ni, and Pb contamination for surface sediments of the Akyatan Lagoon. Additionally, the study results indicated that the calculated hazard index (HI) values ranged from 1.32E-04–1.87E+ 00 whilst the calculated Total Lifetime Cancer Risk (TLCR) values ranged between 1.19E-07 and 3.26E-03 for the adults and children with the higher values calculated for the children, showing a higher potential health hazards for the children. Our study also indicated significant health hazards for children and adults from the carcinogenic Cr, Cu, Mn, Ni, and Pb in the Akyatan Lagoon.