The underlying approach was to identify associations between ASS development and distribution within estuarine geomorphological units. Patterns of ASS distribution and the characteristics of the soils are assumed to be associated with hydro-geomorphic processes that influence soil development. This study utilized a multi-level methodology involving multi-resolution remotely-sensed data and GIS analysis to generate multi-scale hydro-geomorphic information (geomorphic setting, water sources and hydro-dynamics). The method includes the identification of Geo-climatic Regions (GcR), a new estuary classification system, and use of hydro-geomorphic units (HGU) for Central Java to establish a hydro-geomorphology-based classification scheme to aid mapping ASS distribution. Field and laboratory assessment of soil properties were undertaken to identify the vertical and horizontal distribution of ASS of the HGUS in each type of estuary. This study identified four estuary types that represent two GcRs on the north coast: river-dominated estuary (Rambut Estuary); tide-dominated estuary (Jajar Estuary), and two GcRs on the south coast: wave-dominated estuary (Serayu Estuary) and one new type of estuary class which is wave-dominated estuary with pre-existing barrier (Bengawan Estuary). Fifty two HGUs were generated from different types of landforms, land-uses, vegetation types, water table depth and distance from the brackish water resources, from those four selected estuaries. Soil analytical results show that these HGUs represent different ASS physical and chemical properties in coastal sediments especially in the estuary zones of tidal shores and where river deposition occurs. The HGUs in the estuaries on the north coast have less disparity and pyrite concentration,