During  the Plio-Pleistocene times, calcretes and associated palustrine sediments were deposited on the margins of the Nile in Sohag area. These deposits laterally interfinger with narrow peripheral  alluvial fans towards the River Nile margins, wheras towards the center of the basin, they graded into the fluvial systems transverse to the alluvial fans. Overtime, the peripheral carbonate facies were replaced by fluvial systems. The calcretes were fromed as profiles started with nodular grading upward into massive horizons associated with palustrine facies showing variable pedogenic structures such as brecciation, desiccation cracks, mottling, rhizoliths, pseudomicrokarst cavities and lamiinae.

The petrography, facies relations and geochemical data had proved that the calcretes are products of the mixed pedogenic and vadose-phreatic processes associated with the palustrine environments. Palustrine limestones were deposited in a fresh water shallow carbonate lake of low gradients and intense fluctuating margins. The present data had revealed that the calcrete-palustrine facies were probably developed as a result of three main sequential depositional processes; alluvial deposition, calcretization and precipitation of palustrine limestones.

The sedimentological characteristics of the mixed calcrete-palustrine facies associations indicate their accumulation in an intermediate to semi arid climates and conditions of scarce clastic sediment input as well as a continuous elevation of the ground water table, which favored the development of carbonate fringes. In contrast, their absence in some parts of the sequence may be resulted from the increase of clastic supply associating the changes towards the humid climatic conditions. At these times, the fluvial channels had a greater lateral mobility and spreading towards the Nile flanks, replacing the carbonate environments. Subsidence was greater in the central Nile basin than its margins, as proved, by the thick thickness of the Plio-Pleistocene succession of fluvial system in this area. Thus, changes in paleoclimate, topography and the clastic sediment influx on the flanks of the Nile basin were the main controlling factors on the development of the carbonate-clastic sequences, as well as the vertical and lateral variations in the palustrine facies.