As a key environmental parameter to induce radiation dose and effect on non-human species, radioactivity level is rarely evaluated in typical ecosystems of coral reefs, mangroves, and hydrothermal vents. In this study, naturally occurring radionuclides (U, Ra, Ra, and K) in carbonate, silicate, and sulfide sediments collected from coral reefs, mangroves, and hydrothermal vents were simultaneously measured using high purity germanium (HPGe) γ spectrometry. Radioactivity levels and radionuclide fingerprints (Ra/U and Ra/Ra) were interpreted and explored for tracking sources and formation processes of marine sediments in distinct marine ecosystems. Additionally, ionizing radiation dose rate on representative marine biotas (mollusc-bivalve, crustacean, polychaete worm, benthic fish, and pelagic fish) was evaluated using the ERICA tool with an increasing rank in coral reefs < mangroves < hydrothermal vents. Polychaete worm received the highest radiation dose relative to other marine biotas. We also emphasized the dominant contribution of Po to total radiation dose rate on marine biotas.