Zwitterionic Compounds (ZIs) have attracted a lot of attention because of their properties. In contrast to ionic liquids, which consist of separate ions, the ZI structures, with their covalently bound cations and anions, exhibit additional complexity and diversity, which suggests that their ecotoxicological behavior should probably not be extrapolated from that of ionic liquids. This study deals with the aquatic toxicity of ZIs to the bacterium Allivibrio fischeri and the microalgae Raphidocelis subcapitata. 16 ZIs with five different cationic groups (ammonium, imidazolium, pyridinium, pyrrolidinium and piperidinium) and two anionic groups (sulfonate and carboxylate) were examined and the relationships between their structure and toxicity are given. All examined ZIs are harmless or practically harmless for both microalgae and bacteria (mean effective concentration, EC)50 > 100 mg L.−1), which have a significantly lower risk potential for aquatic species than their counterparts to ionic liquids. The results also show that the increased hydrophobicity of ZIs due to the increase in the cation alkyl chain or the spacer length has a significant influence on the EC50 Values for microalgae, which in turn causes higher toxicity. However, when considering the different cationic groups of the ZIs examined, no significant differences were observed, contrary to what is known for the ecotoxicity of the ionic liquids. No relationships were found between the chemical structure of ZIs and EC either50 Values determined for the bacterium A. fischeri. The structural differences between ZIs and ionic liquids lead to different interaction mechanisms with microalgae and bacterial membranes, which may explain why the heuristic rules for ecotoxicity previously given for ionic liquids do not apply to ZIs.