Room temperature ionic liquids (ILs) are non-volatile organic solvents that are considered environmentally-friendly alternatives to traditional industrial solvents. However, the evidence of IL toxicity is mounting, while the mechanisms of toxicity to freshwater organisms remain poorly understood. ILs have been shown to have a wide-ranging toxicity to different taxa of freshwater algae, and differences in algal cell wall composition have been posed as one possible explanation for this variation. The cell wall is known to play a critical role in mediating the transport of materials into and out of algal cells, including potential toxins. The objective of our study was to determine the role of the cell wall in the toxicity of ILs to the freshwater phytoplanktor Chlamydomonas reinhardtii. We exposed wild-type (having a cell wall) and mutant (lacking a cell wall) strains of C. reinhardtii to a range of concentrations of five structurally-different ILs in 96-h standard toxicity bioassays. Our results suggest that the cell wall is involved in determining the susceptibility of C. reinhardtii to some but not all ILs, indicating that other factors, such as the base cation of the IL, are also involved. The alkyl chain length of an IL, a key factor in previous IL toxicity bioassays, does not appear to influence the ability of the cell wall to mitigate IL toxicity. The results of this study have important implications for predicting the effects of ILs in aquatic ecosystems and for extrapolating the effects of ILs across organisms.