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Salt-affected soils play an important role in the Pantanal wetlands ecosystem, in Brazil, but their occurrence on higher landforms is not well understood. In order to investigate the major processes involved in salt-affected soil formation, a trench was opened in a representative transition between the floodplain and a paleochannel-paleolevee complex not currently reached by floodwater. The trench was 6 meter long and 2 meter deep, and 121 soil samples were collected in a 0.25 x 0.25 m regular grid and submitted for soil (particle-size, pH, exchangeable cations) and solution extract (major cation and anions) analyses. Analytical results were subjected to geostatistical and principal components analyses (PCA). For selected horizons, an undisturbed sample was collected to perform thin sections and micromorphology description. The presence of degraded carbonates in the soils indicated an ancient formation. The regional environmental settings of the alluvial fan and particle size variation along the soil profiles suggested that the sediments of the study site were deposited during the Late Pleistocene and Holocene, in a river channel-levee complex and an abandoned channel by avulsion processes. The depressed topography of the abandoned channel, accompanied by moderately drier climates during early Holocene, likely favored low leaching of salts and higher evapotranspiration, enabling the development of salt affected soils. Later erosion of the region, which is expected in older lobes of alluvial fans, triggered a relief inversion in the area, preserving the more clayey areas as a slightly higher landform with remaining salt-affected soils. Currently, the seasonal flooding mainly reaches the footslope of this landform, triggering redoximorphic processes, expressed as redox concentrations and depletions, and solodization processes, expressed by lower values of pH, cation exchange capacity (CEC), base saturation and exchangeable sodium percentage (ESP) than at the summit. Thus, the occurrence of salt-affected soils on higher landforms is the reflection of a complex sedimentological history. In this way, the genesis of salt-affected soils on higher landforms, which seems to be poorly understood in many situations worldwide, should be carefully investigated in order to address formation mechanisms, especially in extremely dynamic environments of tropical wetlands.