The structure of mono- and diprotonated cyclohexyldiamine isomers in aqueous solution is investigated theoretically by the application of the CPCM continuum solvation model combined with the MP2/aug-cc-pVDZ model chemistry. The calculated Gibbs energy of hydration (Delta G(hyd)) is expressed in different terms with physical meaning: cavity formation, solute conformational variation, and solute-solvent interaction. Significant differences of the Delta G(hyd) values are found among isomers, which are interpreted based on the analysis of the factors accounting for the stability of the conformers/isomers in the gas and solution phases. Particular attention is given to the role played by the formation of an intramolecular hydrogen bond in the monoprotonated forms and by the Coulombic repulsion between the NH3+ groups in the diprotonated ones. From the Gibbs energies of the acid/base pairs in the gas phase and respective hydration Gibbs energies, the acidity constants (pK(a)) are calculated and interpreted. For some isomers, the constants are also determined experimentally by potentiometric titration. A good agreement was found between the calculated and experimental values.