In this study, the natural and anthropogenic radioactivity levels in the sediment samples collected from the Marmara Sea in Turkey were determined. The average activity concentrations (range) of 226Ra, 238U, 232Th, 40K and 137Cs were found to be 23.8 (13.8–34.2) Bq kg−1, 18.8 (6.4–25.9) Bq kg−1, 23.02 (6.3–31.1) Bq kg−1, 558.6 (378.8–693.6) Bq kg−1 and 9.14 (4.8–16.3) Bq kg−1, respectively. Our results showed that the average activity concentrations of 226Ra, 238U and 232Th in the sediment samples were within the acceptable limits; whereas the average activity concentration of 40K in the sediment samples was higher than the worldwide average concentration. The average radium equivalent activity, the average absorbed dose rate and the average external hazard index were calculated as 100.01 Bq kg−1, 48.32 nGy h−1 and 0.27, respectively. The average gross alpha and beta activity in the seawater samples were found to be 0.042 Bq L−1 and 13.402 Bq L−1, respectively. The gross alpha and beta activity concentrations increased with water depth in the same stations. The average heavy metal concentrations (range) in the sediment samples were 114.6 (21.6–201.7) μg g−1 for Cr, 568.2 (190.8–1625.1) μg g−1 for Mn, 39.3 (4.9–83.4) μg g−1 for Cu, 85.5 (11.0–171.8) μg g−1 for Zn, 32.9 (9.1–73.1) μg g−1 for Pb and 49.1 (6.8–103.0) μg g−1 for Ni. S5 station was heavily polluted by Cr, Cu, Ni and Pb. The results showed that heavy metal enrichment in sediments of the Marmara Sea was widespread.