Ionic Liquids (ILs) are generically regarded as environmentally "harmless" and thus, assumed as "non-toxic". However, due to the endless design possibilities, their ecotoxicological profile is still poorly known. An accurate knowledge on the toxicity of a substance is required, under the scope of environmental regulation worldwide, before their application and commercialization. Knowledge on the relationship between the chemical structure and toxic effects is essential for the future design of more biocompatible solvents. Focusing on the use of ILs as base lubricants, lubricant additives, or even as potential working fluids for absorption heat pumps, the knowledge on its environmental impact is of great importance, due to the possibility of spills. In this specific context, four analogues of glycine-betaine-based ILs (AGB-ILs) and four glycine-betaine based ILs (GB-ILs) were synthesized and characterized. Their ecotoxicity was assessed using representatives of two trophic levels in aquatic ecosystems, the bacteria Allivibrio fischeri (commonly used as a screening test organism) and the microalgae Raphidocelis subcapitata (as an alternative test organism that has been proven very sensitive to several IL families). The microalgae were more sensitive than the bacteria, hence, following a precautionary principle, we recommend considering the toxicity towards microalgae as an indicator in future studies regarding the focused ILs. Although four of the studied ILs were derived from a natural amino acid, all were considered hazardous for the aquatic environment, disproving the primary theory that all ILs derived from natural compounds are benign. Furthermore, the modification in the structure of anion and the cation can lead to the increase of toxicity.