Surface characterization of polymer inclusion membranes (PIMs) using the polymers cellulose triacetate and polyvinyl chloride, containing different ionic liquids (ILs) as carriers, has been performed. Three different ILs have been tested: commercial trioctyl methylammonium chloride (Aliquat 336–AlqCl−) and two derivatives bearing the counter anion NO3− or SCN− (AlqNO3 and AlqSCN, respectively). Surface analysis was performed by scanning electron microscopy (SEM) and X-ray photoelectron spectroscopy (XPS) for both dry membranes and PIMs immersed for 4 days in ultrapure water to investigate the effect of the interaction of water with the membrane’s morphology and composition. XPS analysis of the PIMs revealed that immersion in ultrapure water causes a decrease in the atomic concentration percentage (A.C.%) of the specific IL atoms (Cl, S, and N) when compared with dry samples. Moreover, SEM images of the PIMs containing the IL AlqNO3 showed an alteration in the morphology of the membrane due to water contact at surface level, whereas no changes were observed at a bulk level. These changes in the surface composition of the water equilibrated PIMs may be associated with the solubilization of the IL in the water solution, which, therefore, may affect the reactivity of the membrane’s surface. To better understand this effect, PIMs containing both AlqCl and AlqNO3 as carriers were used for arsenic (V) transport. It was found that AlqCl was the most effective IL and that the effectivity of the PIM on As(V) removal was not affected after five cycles of the membrane’s reuse.