Several bioassays have been carried out to analyze the toxicity and biodegradability of several imidazolium ionic liquids (ILs) in aqueous phase. The synthetized compounds consist of an imidazolium cation with two alkyl substituents in positions 3 (R1) and 1 (R2) and a counter-ion. The alkyl substituent R1 has been fixed as a methyl group and the effect of the alkyl chain length (C1-C8) of the other substituent (R2) has been tested. Moreover, the influence of diverse counter-ions A- (Cl-, PF6, XSO4-) has been analyzed. Acute toxicity and EC50 values of each compound in the aqueous solution have been determined by using the Microtox standard procedure. Biodegradability of IL has been determined by measuring BOD5 of aqueous samples containing IL and/or D-glucose and the IL residual content and/or d-glucose concentration after this assay. The viability of the microorganisms used in the BOD5 has been related to the ATP in the samples, measured by a bioluminescence assay. All the ILs tested were not biodegradable in the considered conditions. Besides, it was found that the shorter the chain length of side chain R2, the lower the toxic effect is. On the contrary, the anion has a little effect on the IL toxicity.