Geosynthetic Clay Liners (GCLs) serve as vital hydraulic barriers in landfill liners, facing challenges from aggressive ionic solutions that detrimentally impact their performance. This study employs synthetic leachates, comprising various concentrations of ammonium acetate and sodium hydroxide solutions, to replicate real-world conditions over durations of 2, 7, and 15 days. The ionic solutions influence the swelling capacity of sodium bentonite, the primary GCL constituent, through cation exchange, thereby diminishing overall GCL performance. Activation of bentonite through soda ash, a cost-effective and widely utilized method, enhances its performance, leading to improved sodium-activated bentonite utilized as a composite liner material for an activated bentonite GCL. Activated bentonite exhibits significant increases in swell index (66%), liquid limit (9.3%), and plastic limit (8%) compared to non-activated counterparts, attributed to heightened monovalent Na+ ions. The activated bentonite GCL demonstrates a substantial 47-fold decrease in hydraulic conductivity, indicating superior hydraulic barrier performance. Tests with synthetic leachates confirm the activated sodium bentonite’s heightened resistance to aggressive leachates. Hydraulic conductivity in both ammonium acetate and sodium hydroxide solutions exhibits concentration-dependent increases but decreases with permeation duration, illustrating the bentonite’s affinity for ammonium ions and the pH-dependent effect on hydraulic conductivity. Adsorption studies reveal decreased adsorption with increasing ammonium ion concentration and increased adsorption with NaOH concentration. The study underscores the adverse effects of basic pH and ionic concentrations on GCL, highlighting the potential for improvement through the strategic use of activated bentonite, showcasing heightened resilience against environmental challenges.