The development of inorganic membranes has mainly found applicability in liquid separation technologies. However, only a few reports cite the permeation and separation of liquids through inorganic nanofiltration membranes compared with the more popular microfiltration membranes. Herein, we prepared silica membranes using 3,3,3-trifluoropropyltrimethoxysilane (TFPrTMOS) to investigate its liquid permeance performance using four different ion solutions (i.e., NaCl, Na2SO4, MgCl2, and MgSO4). The TFPrTMOS-derived membranes were deposited above a temperature of 175 °C, where the deposition behavior of TFPrTMOS was dependent on the organic functional groups decomposition temperature. The highest membrane rejection was from NaCl at 91.0% when deposited at 200 °C. For anions, the SO42− rejections were the greatest. It was also possible to separate monovalent and divalent anions, as the negatively charged groups on the membrane surfaces retained pore sizes >1.48 nm. Ions were also easily separated by molecular sieving below a pore size of 0.50 nm. For the TFPrTMOS-derived membrane deposited at 175 °C, glucose showed 67% rejection, which was higher than that achieved through the propyltrimethoxysilane membrane. We infer that charge exclusion might be due to the dissociation of hydroxyl groups resulting from decomposition of organic groups. Pore size and organic functional group decomposition were found to be important for ion permeation.