Salorthidic Fluvaquents originating from Seville, Andalusia, were sampled and subjected to rheological and particle charge investigations. Structural changes in a managed and a natural site under pasture were compared based on physicochemical laboratory analyses, scanning electron microscopy, particle charge density (PCD) measurements, and rheological tests. An uncultivated site located at the riparian zone of the Guadalquivir River showed a natural fluvio-marine-affected development. A regular influx and exchange of salts in the groundwater, especially in the form of NaCl and calcite, dominate soil genetic processes. In contrast, drainage of the saline-sodic soils for cultivation, furrow irrigation, and phosphogypsum fertilization have led to a modification of the salinity gradients throughout the reclaimed soil profile. Sodium ions on the exchangers were released due to the Ca amendment, which led to a decreased exchangeable Na+ concentration (exchangeable Na percentage [ESP] < 15) in the topsoil. The soil microstructure of the carbonate-rich and clayey soil remained stable, and surface sealing and crusting were reduced, particularly in the Ap horizon. Results from PCD measurements, derived zeta potential, ζ, and the rheological parameters loss factor tanδ and integral z were consistent. Comparing reclaimed and natural conditions, the rheological parameters integral z and ζ potential showed a linear correlation to ESP and the cation ratio of soil structural stability. This was indicated by increased integral z values and ζ potentials, showing a trend toward stable agglomeration and increased microstructural strength in the case of the ameliorated reclaimed topsoil. Phosphogypsum amelioration was appraisal as successful using approach.