Airborne aerosols were collected in six size classes (PM<0.1, PM0.1–0.5, PM0.5–1, PM1–2.5, PM2.5–10 and PM>10) to investigate aerosol health risks in remote and industrial areas in Japan. We focused on heavy metals and their water-dispersed fractions. The average concentration of heavy metals was 18 ± 25–86 ± 48 ngm−3 for PM<0.1, 46 ± 19–154 ± 80 for PM0.5–1 ngm−3, 98 ± 49–422 ± 186 ngm−3 for PM1–2.5, 321 ± 305–1288 ± 727 ngm−3 for PM2.5–10 and 65 ± 52–914 ± 339 ngm−3 or PM>10, and these concentrations were higher in industrial areas. Heavy metals emitted from domestic anthropogenic sources were added to the long-range transport component of the aerosols. The water-dispersed fraction of heavy metals contained 3.3–40.1% of the total heavy metals in each size class. The relative contribution of Zn and other species (As, Cd, Cr, Ni, Pb, Mn, V and Cu) increased in the water-dispersed fraction. Smaller particles contained greater proportions of the water-dispersed heavy metal fraction. Carcinogenic risk (CR) and the hazard index (HI) were estimated for each size class. The CR of carcinogens was at acceptable levels (<1 ×10−6) for five particle size fractions. The HI values for carcinogens and noncarcinogens were also below acceptable levels (<1) for the same five size fractions. The estimated CR and HI values were dominated by contributions from the inhalation process.