Because of wide applications of surface-modified zinc oxide nanoparticles (ZnO-NPs) in commercial sunscreens and their easiness of being released into water, concerns have been raised over their potential effects on aquatic organisms. This study compared physicochemical properties of silane-coated and uncoated ZnO-NPs to elucidate their toxic potencies toward three freshwater and three marine microalgae. Surfaces of ZnO-NPs (20 nm) were modified by coating with 3-aminopropyltrimethoxysilane (A-ZnO-NPs) that provides the particles with a more hydrophilic surface, or dodecyltrichlorosilane (D-ZnO-NPs) that turns the particles to hydrophobic. Uncoated ZnO-NPs formed larger aggregates and released more Zn2+ than did either of the two coated ZnO-NPs. The three nanoparticles formed larger aggregates but released less Zn2+ at pH 8 than at pH 7. Although sensitivities varied among algal species, A-ZnO-NPs and uncoated ZnO-NPs were more potent at inhibiting growth of algal cells than were D-ZnO-NPs after 96-h exposure to ZnO, uncoated ZnO-NPs, each of the coated ZnO-NPs or ZnSO4 at 10 concentrations ranging from 0.1 to 100 mg/L. The marine diatom Thalassiosira pseudonana exposed to ZnO-NPs, A-ZnO-NPs or D-ZnO-NPs resulted in differential expressions of genes, suggesting that each of the coatings resulted in ZnO-NPs acting through different mechanisms of toxic action.