While multimodal (MM) chromatography is a promising approach for purifying proteins, the lack of a fundamental understanding of how ion-ligand interactions govern selectivity limits its use in the biopharmaceutical industry. This study uses molecular dynamics simulations to study the interactions between simple monovalent cations and two commonly used structurally similar multimodal chromatography ligands, the Capto ligand and Nuvia cPrime, immobilized on the surface. On the Capto ligand surface, ion presence and type play a key role in modulating the formation of phenyl rings and carboxylate clusters. The flexible linkage attaching the Capto ligand to the self-assembled monolayer (SAM) surface allowed multiple ligands to form interactions with the small cations, while large cations interacted less strongly, following the order Li+ > Na+ > K+ > Cs+. Thus, smaller cations resulted in greater ordering on the surface and lower ion diffusivities, while larger cations resulted in less ordering and higher ion diffusivities, following the order Li+ < Na+ < K+ < Cs+. In contrast, due to the rigid attachment of Nuvia cPrime to the SAM surfaces, the cations bound less strongly and had a much smaller effect on ligand clustering or ordering. Additionally, ions in the presence of the Nuvia cPrime surface had generally greater diffusivities than those in the presence of the Capto ligand. Overall, the interaction of cations with the multimodal ligands can lead to unique configurations on the SAM that likely contribute to differential behavior in biological separations.