Interest in ionic liquids for their potential in different chemical processes is increasing, as they are claimed to be environmentally benign and are very good non-volatile solvents for a wide range of applications. With regard to their physical and chemical characteristics, the properties of ionic liquids can be modified over a wide range because the cation's fine structure and the anion's identity can be altered. Since millions of ion combinations are possible it is of the highest importance to outline rational guidelines to develop technologically suitable but also environmentally harmless ionic liquids. This paper presents the results of a preliminary assessment of the toxicity of selected imidazolium ionic liquids towards marine algae. The selection of chemical entities was based on the t-SAR approach (thinking in terms of structure-activity relationships) focusing on the length (C(2)<R1<C(6)) or type (aliphatic-aromatic) of the side chain whereas head group (imidazolium) remained the same. The acute effect of ionic liquids was measured using the green alga Oocystis submarina and the diatom Cyclotella meneghiniana inhabiting the southern Baltic Sea. Standard algal testing procedures revealed significant differences in the responses of the two species. O. submarina appeared to acclimatize to the lower concentrations used: after ca. 5 days their ability to grow recovered, and initial densities were eventually restored. In the case of C. meneghiniana, growth in batch cultures was effectively inhibited throughout the experiment regardless of the ionic liquid concentration applied. Additionally, it was found that at higher salinities, the toxicity of 1-butyl- and 1-hexyl-3-methylimidazolium entities towards O. submarina was significantly lower than at low salinities.