Sulfonated calixarenes have long been used as effective binders of ammonium ions in aqueous solution. Recently, the utility of sulfonated calix[4]arenes and calix[6]arenes as specific agents for binding biologically important ammonium ions, and especially post-translationally methylated amino acids, peptides, and proteins, has suggested that they might have important roles to play in the control and understanding of biological pathways. We report here binding data in various buffer systems that attempt to shed light on the roles of buffer and salt in the recognition processes of these hosts. We also report studies on trimethyllysine binding that explore the effects of near physiological salt concentrations and temperatures. These studies provide an understanding of disparate data on these systems and also demonstrate the ability of a sulfonated calixarene to bind trimethyllysine strongly under aqueous conditions that closely replicate the salt concentrations, pH, and temperature of the human body.