In this work, novel and non-toxic fluorinated ionic liquids (FILs) totally miscible in water that could be used in biological applications, where fluorocarbon compounds present a handicap because their aqueous solubility (water and biological fluids) is in most cases too low, have been investigated. The self-aggregation behavior of perfluorosulfonate-functionalized ionic liquids in aqueous solutions has been characterized using conductometric titration, isothermal titration calorimetry (ITC), surface tension measurements, dynamic light scattering (DLS), viscosity and density measurements and transmission electron microscopy (TEM). Aggregation and interfacial parameters have been computed by conductimetry, calorimetry and surface tension measurements in order to study various thermodynamic and surface properties which demonstrate that the aggregation process is entropy-driven and that the aggregation process is less spontaneous than the adsorption process. The novel perfluorosulfonate-functionalized ILs studied in this work show improved surface activity and aggregation behavior, forming distinct self-assembled structures.