Clay-amended barriers are widely used to prevent hazardous leachate percolation from landfill to subsurface. The performance of these barriers is mostly evaluated through numerical simulations with limited experimental investigation through leachate flushing experiments. To bridge this gap, contaminant loading and its flushing experiments were carried out to assess the performance of clay-amended composite materials as landfill liners. River sand (Sa), loamy soil (Ns), and alternative waste materials like fly ash (Fa) and flushed silt (Si) were used to prepare the composites. Composites fulfilling the hydraulic conductivity (<10−7 cm/s) and compressive strength (200 kPa) criteria were selected for contaminant loading and its flushing experiments to understand the fate of fluoride ions. The experimentally determined hydraulic conductivity (Ks) values for all the composites were in the order of 10−8 cm/s. The experimental breakthrough curves exhibited skewed shape, long tailing, and dual peaks. Dual porosity and dual permeability with immobile water models were employed to simulate these curves, revealing that preferential flow pathways and random chemical sorption sites significantly affect solute transport in clay-amended barriers. Further, scanning electron microscopy and energy-dispersive X-ray spectroscopy were employed to trace the preferred path of fluoride ions through the barrier. The removal efficiency and temporal moments were used to determine the percentage mass retained, mean arrival time, and spreading within the barrier. The highest solute mass was retained by sand-clay barrier (SaB30) (91%), followed by loam-clay barrier (NsB30) (59%), fly ash-clay barrier (FaB30) (38%), and silt-clay barrier (SiB30) (4%) with the least mass. The lowest mean arrival time was calculated for NsB30 (269 h) and the highest for SaB30 (990 h), with FaB30 (384 h) and SiB30 (512 h) having values in between. This study concludes that validating the design hypothesis of clay-amended barriers through contaminant loading and its flushing studies leads to an effective and sustainable design.