A systematic study of the effects of hydrophilic ionic liquids concentration and nature (alkyl chain length and type of anion) on the activity of Candida antarctica lipase B is here reported. The increase in the concentration of the studied ionic liquids is shown to cause a decrease of the enzyme activity, but the effect is dependent on the ionic liquid used. This behavior is partially due to the ionic liquid impact on the thermodynamic water activity, but direct interactions between the hydrophilic ionic liquid and the enzyme are also disclosed. Cations with longer alkyl chains decrease the enzyme activity by obstruction of its non-polar active site, while direct interactions established between the enzyme and the anions, dominated by dispersion forces and hydrogen-bonding, contribute also for the loss of activity observed.