In this work, we demonstrate that the presence of fluorinated alkyl chains in Ionic Liquids (ILs) is highly relevant in terms of their thermophysical properties and aqueous phase behaviour. We have measured and compared the density and viscosity of pure 1-ethyl-3-methylimidazolium tris(pentafluoroethyl)trifluorophosphate, [C2C1im][FAP], with that of pure 1-ethyl-3-methylimidazolium hexafluorophosphate, [C2C1im][PF6], at atmospheric pressure and in the (288.15 to 363.15) K temperature range. The results show that the density of [C2C1im][PF6] is lower than that of [C2C1im][FAP], while the viscosity data reveal the opposite trend. The fluid phase behaviour of aqueous solutions of the two ILs was also evaluated under the same conditions and it was found that the mutual solubilities of [C2C1im][FAP] and water are substantially lower than those verified with [C2C1im][PF6]. The experimental data were lastly interpreted at a molecular level using Molecular Dynamics (MD) simulation results revealing that the interactions between the IL ions and the water molecules are mainly achieved via the six fluorine atoms of [PF6]− and the three analogues in [FAP]−. The loss of three interaction centres when replacing [PF6]− by [FAP]−, coupled with the bulkiness and relative inertness of the three perfluoroethyl groups, reduces its mutual solubility with water and also contributes to a lower viscosity displayed by the pure [FAP]-based IL as compared to that of the [PF6]-based compound.