Water infiltration through unsaturated soil is a crucial parameter for accurately modelling contaminant transport, groundwater recharge, and geo-structural stability. Soils are naturally deposited in horizons, but in design and analysis, the horizons are often overlooked, and layered soil systems are approximated as homogeneous soil profiles. Infiltration characteristics through homogeneous soils have been extensively studied, but infiltration through varved clays, which is a special case of layered soil structure, has gained little attention. Varved clays are unique soil deposits formed by the sequential alternate deposition of two significantly differently textured soils. The objective of this study is to evaluate the temporal infiltration characteristics of reconstituted varved clay profiles and compare their infiltration behaviour with homogeneous profiles for two different matric suction heads of − 2 and − 5 cm. To accomplish this objective, a vertical one-dimensional infiltration test is carried out on four soil profiles in the laboratory using a minidisc infiltrometer (MDI). For the analyses, two soils, red soil (RS) and black soil (BS), are chosen. Two homogeneous profiles are created by filling the soil moulds entirely with RS and BS, respectively. To simulate varved clay, the two chosen soils are placed interchangeably one over the other. The study reveals that soil type, variation in suction head, and the sequence of placement laminae in varved clays significantly affect the infiltration through the soil profile.