A proper understanding of radioactive contamination levels of food resources near the Fukushima Dai-ichi Nuclear Power Plant is necessary to estimate the potential effects of radionuclide contamination on human health. This study was conducted to present a direct comparison of radiocesium (134Cs and 137Cs) concentrations in marine and freshwater fish inhabiting different water bodies in Fukushima Prefecture (coastal waters, 6.3-54.5 km from the plant; forest rivers and irrigation ponds, 1.4-71.6 km), and to reveal plausible contamination mechanisms for each habitat. In contrast to marine demersal fish (7 species, n = 50), which showed lower and less variable radiocesium concentrations (0.234-3.41 Bq kg-1-wet), freshwater fish (6 species, n = 463) showed higher and more site-specific variations for each species and habitat (4.09 Bq kg-1-wet - 25.6 kBq kg-1-wet) in 2015-2016. The apparent concentration ratio (aCR, L/kg) of 137Cs in fish to water is higher for fish of freshwater habitats (mean 1240-12900 for each site) than in those of coastal waters (mean 200). Radiocesium contamination is more severe and persistent in freshwater fish, especially those distributed within the designated evacuation zone (salmon in rivers and bass in ponds). Continuous radiocesium uptake through the food web in relation to fish feeding habits and size (size effect), and biotic/abiotic characteristics in water and surrounding environments are main factors affecting site/habitat-specific bioaccumulation of radiocesium in freshwater fish. By contrast, uniformly lower radiocesium concentrations in marine demersal fish are mainly attributable to decreased radiocesium transfer intensity from the benthic food web because of lowered radiocesium contamination in sediments, and low physiological ability to retain radiocesium. Our results revealed a strong contrast of radiocesium contamination levels and mechanisms between marine and freshwater fish in natural habitats. Particularly, a close relation between 137Cs accumulation in river salmon and contamination of prey items in forest ecosystems (mainly terrestrial and aquatic insects) is peculiar to the upstream areas affected by the Fukushima accident.