In this study, the influence of different head groups, functionalised side chains and anions of ionic liquids on the marine bacteria Vibrio fischeri, the limnic green algae Scenedesmus vacuolatus and the fresh water plant Lemna minor was investigated. The aim of these experiments is to improve the knowledge base for the molecular design of ionic liquids leading to a reduced (eco)toxicological hazard potential. The analysed set of about 40 ionic liquids confirmed the interdependency between lipophilicity—as derived from gradient HPLC—and (eco)toxicity. The toxicity was clearly reduced for the test organisms (partially by six to seven orders of magnitude) when short functionalised side chains were used instead of non-polar alkyl chains. Furthermore, we could demonstrate strong interactions of hydrophobic ionic liquid cations with two different types of common biological lipidbilayers, indicating that the membrane system of organisms is probably a primary target site of toxic action. These systematic studies are addressed to producers, developers and downstream users of ionic liquids in different fields of application, to facilitate the selection of (eco)toxicologically favourable structural elements and thus to contribute to the design of inherently safer ionic liquids.