Nanoparticles (NPs) are widely used in many industrial applications. NP fate and behavior in seawater are a very important issue for the assessment of their environmental impact and potential toxicity. In this study, the toxic effects of two nanomaterials, silicon dioxide (SiO2) and titanium dioxide (TiO2) NPs with similar primary size (~20 nm), on marine microalgae Dunaliella tertiolecta were investigated and compared. The dispersion behavior of SiO2 and TiO2 NPs in seawater matrix was investigated together with the relative trend of the exposed algal population growth. SiO2 aggregates rapidly reached a constant size (600 nm) irrespective of the concentration while TiO2 NP aggregates grew up to 4 ± 5 μm. The dose–response curve and population growth rate alteration of marine alga D. tertiolecta were evaluated showing that the algal population was clearly affected by the presence of TiO2 NPs. These particles showed effects on 50 % of the population at 24.10 [19.38–25.43] mg L−1 (EC50) and a no observed effect concentration (NOEC) at 7.5 mg L−1. The 1 % effect concentration (EC1) value was nearly above the actual estimated environmental concentration in the aquatic environment. SiO2 NPs were less toxic than TiO2 for D. tertiolecta, with EC50 and NOEC values one order of magnitude higher. The overall toxic action seemed due to the contact between aggregates and cell surfaces, but while for SiO2 a direct action upon membrane integrity could be observed after the third day of exposure, TiO2 seemed to exert its toxic action in the first hours of exposure, mostly via cell entrapment and agglomeration. © 2015, Springer-Verlag Berlin Heidelberg.