Nano thin films of Nafion® and poly(vinyl alcohol) (PVA) were successfully assembled into layer-by-layer (LBL) films at 1.2 ≤ pH ≤ 1.3. Sequential self-assembly of PVA/Nafion® was monitored using FTIR, AFM, and Ellipsometry where the average bilayer thickness for a 20 bilayer film measured 315 A, surface roughness of 550 A, a contact angle of 112°, and resisted degradation up to pH = 10. In the mechanism of self assembly we considered segmental hydrophobic interactions (SHI) and fluorinated hydrogen bonding (FHB) of the type (C–F: → H–N) and (C–F: → H–O) as potential interactions between Nafion® segments and either poly(vinyl alcohol) (PVA) at pH = 1.2 or poly(allylamine hydrochloride) (PAH) at pH ≥ 11. Our experiments on self-assembly monitored the ionization of polyelectrolytes (PE) couples using colorimetric analysis, ATR-FTIR, zeta potential and changes in FTIR peak shifts imposed on the O–H and N–H str, N–H asym str, and the CF2band. PE couples of PAH/Nafion®, PAH/poly(styrene sulfonic acid) PSS, and PVA/PSS were used as cross references to justify FHB versus SHI in the self-assembly of PVA/Nafion®(pH = 1.2) and PAH/Nafion®(pH ≥ 11). The ultra thin acidic PVA/Nafion® LBL film (0.05 to 0.1 μm) is a competitive alternative to the thick PVA/Nafion® blend membranes (50 to 500 μm) and would have potential application in the design of advanced fuel cell, battery, and detection systems.