To deduce the prevailing paleoenvironmental conditions during the deposition of the Plio-Pleistocene continental carbonate sequence at Wadi El-Natrun (NW Egypt), we examined and compared the macro- and micro-morphological, mineralogical and stable isotopic characteristics of calcretes, dolocretes, palustrine carbonates, and silcretes of the lower Pliocene Meikheimin and Plio-Pleistocene Qataji formations. Calcrete occurs in both formations and exhibits a variety of forms, including powdery, nodular, fracture-infill, massive and hard laminated crusts (hardpan). The calcretes developed in mixed vadose and phreatic diagenetic environments under an arid to semi-arid climate. Palustrine carbonates occur in the upper Qataji Formation and developed as nodular, desiccated, brecciated, mottled and pisoidal limestones that are interbedded with the calcretes. They exhibit varied micro-morphological features, including circum-granular and planar cracks, nodular and clotted fabrics, peloidal textures, infilling of burrows, root molds, and fenestral pores, which indicate modifications during subaerial exposure. The dolocrete facies in the upper Qataji Formation comprises laminated carbonate crusts. These include spheroidal dolomite and dolomicrite with Mg-rich clays that formed as primary precipitates in a continental setting. The silcretes consist of spheroidal, irregular opaline accumulations that formed as replacements of calcrete and dolocrete. These features reflect silicification in near-surface environments where there was an interplay between vadose and phreatic environments during deposition and early burial diagenesis. The stable isotopic data suggest deposition under warm, seasonally arid to semi-arid climatic conditions in an area dominated by C3 vegetation. The regional water table was higher in the early Pleistocene than during the early Pliocene but was subject to large fluctuations.