<p>Despite extensive studies of clogging during artificial recharge, the influence of porous-media stratification on clogging remains uncertain. This study conducted sand-column infiltration experiments to evaluate how contrasting grain size layering configurations affect permeability decline, clogging rate and extent, and suspended particle transport and retention. Tested configurations comprised homogeneous and heterogeneous sand columns, including two-layer structures with an upper coarse-grained layer over a lower medium-grained layer (C-M) and an upper coarse-grained layer over a lower fine-grained layer (C-F), and three-layer “sandwich” structures with coarse-medium-coarse (C-M-C), coarse–fine-coarse (C-F–C) and medium-fine-medium (M-F-M) sequences. Results show that the interfacial effects in the stratified columns significantly influenced clogging: Zones adjacent to layer interfaces tend to provide both the onset locations and primary clogging regions, thereby governing the rate and extent of clogging. The influence of interfacial effects on clogging was also governed by the degree of median grain-size contrast across interfaces and the thickness of the finer-grained stratum. For instance, the double-layer and “sandwich” column structures indicate that the greater the grain size contrast across layered interfaces, the more pronounced the interfacial effects become during clogging. Furthermore, the C-M-C results demonstrate that when the medium-grained sand layer thickness decreases, the interfacial effects become significantly weaker compared to C-M and C-F–C structures. This study verifies the interface effect on clogging based on the spatial distribution of suspended particle deposition in porous media and analyzes the underlying mechanisms, which provide theoretical foundations for optimizing permeability regulation in managed aquifer recharge in stratified hydrogeological settings.</p>