Microalgae-based water treatments for the removal of different types of pollution have been gaining considerable attention during the last few decades. However, information about microalgae potential in the removal of pharmaceuticals and personal care products (PPCPs) and the ecotoxicological outcomes is still limited. Therefore, in this work, we aimed at investigating salicylic acid removal from water by three different microalgae strains, namely Chlorella sorokiniana, Chlorella vulgaris and Scenedesmus obliquus. For such a purpose, photobioreactors were operated under batch and semi-continuous mode. Apart from determining the reduction in the concentration of salicylic acid attained by each strain, we used zebrafish embryo bioassays to assess the efficiency of microalgae to reduce its toxicity effects. S. obliquus was the strain that achieved the most significant decrease in the concentration and toxic effects of salicylic acid. Indeed, S. obliquus was able to rescue mortality and reduce abnormalities at practically 100%. The efficiency of C. sorokiniana and, especially, that of C. vulgaris were not so remarkable, indicating that the removal of SA and its toxic effects from water by microalgae is markedly strain dependent. The obtained results proved the importance of considering toxic effects for a more comprehensive evaluation of microalgae efficiency in the removal of PPCPs in view of an adequate selection for water treatment.