In this study, we present surface-enhanced Raman spectroscopy (SERS) investigations of five analogs of a novel group of N-benzylamino(boronphenyl)methylphosphonic acids: N-benzylamino-(3-boronphenyl)-S-methylphosphonic acid (m-PhS), N-benzylamino-(4-boronphenyl)-S-methylphosphonic acid (p-PhS), N-benzylamino-(2-boronphenyl)-R-methylphosphonic acid (o-PhR), N-benzylamino-(3-boronphenyl)-R-methylphosphonic acid (m-PhR), and N-benzylamino-(4-boronphenyl)-R-methylphosphonic acid (p-PhR) deposited onto 10-nm gold nanoparticles in an aqueous solution at physiological pH (pH = 7). In addition, for the p-PhR molecule, the SERS spectra in the various conditions of pH levels of the solutions (from pH = 3 to 11) and phosphonic acid concentration (10−3–10−5 M) were measured. In general, the SERS spectral profiles indicate that at pH = 7, all of the aforementioned molecules interact with the colloidal gold surface via a boronphenyl ring. However, the orientation of the boronphenyl ring onto the substrate surface is different for each of the studied molecules. The boronic acid group of p-PhS and p-PhR binds to the gold nanoparticles, whereas the phosphonic acid group assists in the interaction with the substrate for p-PhR only. For all the molecules, the –CLCα(P)N– fragment distinctly influences the molecule/gold interactions, especially in the case of o-PhR. The previous differences in the compound behavior at the gold/liquid interface underline the role of an absolute configuration (–R and –S) and a type of isomer (orto-, meta-, and para-) on the SERS signals, which means their influence on the adsorbate geometry. Additionally, based on the SERS results for p-PhR in various environmental conditions, we draw conclusions about spectral changes (adsorbate geometry changes) as a result of the pH of solution and molecule concentration alternations.