In the Ganges River basin, studies related to the depth-wise distribution of major and trace metals in these floodplain soils (seasonally waterlogged and non-water logged) have been limited thus far. This research attempts to address this gap in the current literature by geochemical and geostatistical analyses and assessment of soil pollution. Significant concentrations of major and trace metals in these soils could greatly impact the health of local communities. Soil samples were collected in the eastern Ganges basin from a shallow seasonally waterlogged (SWL) site and a shallow non-waterlogged (SNWL) site up to 3 m below ground level (mbgl) and a deep seasonally waterlogged (DWL, up to 14 mbgl) site. The soils were analysed to determine soil texture and the concentration of major oxides and trace metals with increasing depth. The average concentration of trace metals (Ba, Rb, V, Cr, Ni, As, Pb, Ga, Co, Cs, Nb, W) and major oxides (Al2O3, Fe2O3, K2O, MgO) are higher in the SWL soil than the SNWL soil. A higher concentration of metals generally occurred in the upper soil layers due to the adsorption of elements by the silt and clay fractions. Soil pollution assessment indicated that W, As, Sb and Cu are enriched in both the waterlogged and non-waterlogged soils, while Sn is enriched in the SNWL soil profile only. The values obtained for the geochemical indices, which were geoaccumulation index (Igeo), enrichment factor (EF), contamination factor (CF) and pollution load index (PLI), were relatively higher in the top layers for the SWL and DWL sites. Based on effects range-low (ERL) and effects range-median (ERM) values, the possibility of adverse biological effects caused by the metals is highest for Ni in the DWL site, Cr and Ni in the SWL site and Cu in the SNWL site. Pearson’s correlation and principal component analysis (PCA) justify the role of soil texture, phyllosilicates, Fe-Mn oxyhydroxides and carbonates in the occurrence and distribution of metals in these soils. Seasonal waterlogging facilitates the dissolution and precipitation of oxides, hydroxides, carbonates and adsorption/desorption processes, leading to the accumulation and retention of more trace metals in the soil. This study implies that the silt and clay present in the vadose zone may act as a filter to protect local groundwater aquifers from metal contamination. This work provides insights on the behaviour of major and trace metals in the soil depth profile of seasonally waterlogged floodplain soil that is used for local agriculture.