Molecules containing vibrational Stark shift reporters provide a useful tool for measuring DC electric fields in situ. To quantify this effect theoretically, density functional theory (DFT) calculations are usually utilized in a uniform electric field. However, using a combined theoretical and experimental study, we demonstrate here that uniform field DFT cannot simultaneously model the behavior of the three strongest vibrational modes in molecules forming a monolayer on an electrode. We show, by directly modeling ionic movement, that the measured Stark shifts are explained by partial electrical double-layer penetration into the molecular layer. This effect is sensitive to the local environment, and the Stark shifts can be fully suppressed experimentally by introducing a mixed molecular layer that prevents ionic double-layer penetration.