Polyethyleneimine (PEI) is a widely used polymer in catalysis, gas separation, water treatment, drug delivery, textiles, and paper production. Carbon dioxide can act as a molecular stimulus for amine-rich polymers such as PEIs, a property that has been exploited in CO₂-mediated desalination. This process entails amine-mediated CO₂ capture and the in situ formation of bicarbonate ions, which subsequently undergo ion exchange with chloride ions present in both model and real seawater. In this study, we prepared a series of alkylated PEIs with different chainlengths (C4-C18) and degrees of alkylation (10-40% alkylation) via simple alkylation as previously reported. The obtained hydrophobic PEI, specifically PEI-C16, was further investigated in terms of its crystalline structure using powder X-ray diffraction, small-angle X-ray scattering, thermogravimetric analysis, and inelastic neutron scattering. Based on our analysis, we conclude that the subtle structural changes of hydrophobic poly(ethyleneimine)s were induced by acid-mediated protonation and ion exchange, while the polymer maintained its integrity across multiple desalination cycles. These findings advocate for the employment of hydrophobic poly(ethyleneimine) in CO₂-responsive processes and carbon capture applications.