The 2021 Cyclone Seroja was a category 3 storm that made landfall on Lembata Island, causing extensive damage. This study aims to identify key interpretations of sediment transport related to tropical cyclones (TC) Seroja and past floods using a geopedological approach, estimate the return period through frequency analysis, and determine the rainfall threshold for flooding using HEC-RAS software. Extreme rainfall data from global precipitation model (GPM) (2000-2023) in Wei Laing watershed were analysed alongside LiDAR terrain data, physical and chemical properties of soil, and land cover data. Based on geopedological analysis, the result shows that the erosional-transfer zone of Wei Laing Watershed has thin, loamy, and slightly sandy soils due to erosion and limited pedogenesis. The depositional zone contains flood deposits with abrupt vertical texture changes, reflecting transported coarse grains and finer in-situ sediments. The modern flood deposit (TC Seroja flood deposit) was identified by texture, CaCO3 content, organic matter, and coarse organic material. The fine-grained flood deposits (<_ 4 cm) are classified as slackwater deposits, consist of silty clay loam and silt loam textures, reflecting deposition under slow-flowing conditions. TC Seroja corresponds to a 50-year return period. Hydrological modelling indicates a 60 mm/day rainfall threshold for flooding, with 77 flood events recorded between 2000-2023. The model is confirmed by thick past flood deposits enriched with coarse organic materials. These findings provide insight into flood dynamics and sedimentary responses, supporting future flood risk mitigation efforts.