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Flooded ecosystems are conditioned to seasonal floods that promote specific soil conditions, such as low oxygen, hydromorphism, and peculiar chemical reactions. These environments are dependent on flood pulses that determine specific ecological conditions. Ipucas are seasonally flooded discontinuous forest patches that occur exclusively in the Araguaia Plain in Central Brazil. They are located 0.40 to 1.20 m lower than the surrounding plain, which promotes an accumulation of rainwater for five to six months of the year, being entirely or partially dry during the dry season. The aim of this study was to evaluate the horizontal (centre and edge) and vertical (depths: 0–0.20 m and 0.20–0.40 m) variability of physicochemical parameters in Ipucas soils, attempting to establish the importance of flood pulses and the leaching of surrounding areas in soil formation and composition. Samples were collected during the dry season in three Ipucas of similar size and circularity using a Dutch auger. The results reveal that flood pulses promote the deposition of sediments eroded from the surrounding plain, homogenizing the characteristics of the surface soil, from the edge to the centre of the Ipucas. However, biogeochemical processes, also linked to temporary flooding, account for the differences between the surface and deeper soil horizons because anoxic conditions during flooding promote chemical reactions characteristic of anaerobic environments, modifying the pH and organic matter content, in addition to the gleying of soils subjected to flooding, which are then covered by sediments after the dry season. Finally, Ipucas soils are susceptible to anthropic changes and are dependent on seasonal flood pulses.