Cholinium-based ionic liquids are quaternary ammonium salts with a wide range of potential industrial applications. Based on the fact that the cholinium is a complex B vitamin and widely used as food additive, the cholinium-based ionic liquids are generically regarded as environmentally “harmless” and thus, accepted as “non-toxic”, although their ecotoxicological profile is poorly known. This work provides new ecotoxicological data for ten cholinium-based salts and ionic liquids, aiming to extend the surprisingly restricted body of knowledge about the ecotoxicity of this particular family and to gain insight on the toxicity mechanism of these compounds. The results reported here show that not all the cholinium tested can be considered harmless towards the test organism adopted. Moreover, the results suggest that the cholinium family exhibits a different mechanism of toxicity as compared to the imidazolium ionic liquids previously described in the literature.