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The Pliocene aquifer receives inflow of Miocene and Pleistocene aquifer waters in Wadi El Natrun depression. The aquifer also receives inflow from the agricultural activity and septic tanks. Nine sediment samples were collected from the Pliocene aquifer in Wadi E1 Natrun. Heavy metal (Cu, Sr, Zn, Mn, Fe, Al, Ba, Cr, Ni, V, Cd, Co, Mo, and Pb) concentrations of Pliocene aquifer sediments were investigated in bulk, sand, and mud fractions. The determination of extractable trace metals (Cu, Zn, Fe, Mn, and Pb) in Pliocene aquifer sediments using sequential extraction procedure (four steps) has been performed in order to study environmental pathways (e.g., mobility of metals, bounding states). These employ a series of successively stronger chemical leaching reagents which nominally target the different compositional fractions. By analyzing the liquid leachates and the residual solid components, it is possible to determine not only the type and concentration of metals retained in each phase but also their potential ecological significance. Cu, Sr, Zn, Mn, Fe, and Al concentrations are higher in finer sediments than in coarser sediments, while Ba, Cr, Ni, V, Cd, Co, Mo, and Pb are enriched in the coarser fraction. The differences in relative concentrations are attributed to intense anthropogenic inputs from different sources. Heavy metal concentrations are higher than global average concentrations in sandstone, USEPA guidelines, and other local and international aquifer sediments. The order of trace elements in the bulk Pliocene aquifer sediments, from high to low concentrations, is Fe > Al > Mn > Cr > Zn > Cu > Ni > V > Sr > Ba > Pb > Mo > Cd > Co. The Pliocene aquifer sediments are highly contaminated for most toxic metals, except Pb and Co which have moderate contamination. The active soluble (F0) and exchangeable (F1) phases are represented by high concentrations of Cu, Zn, Fe, and Mn and relatively higher concentrations of Pb and Cd. This may be due to the increase of silt and clay fractions (mud) in sediments, which act as an adsorbent, retaining metals through ion exchange and other processes. The order of mobility of heavy metals in this phase is found to be Pb > Cd > Zn > Cu > Fe > Mn. The values of the active phase of most heavy metals are relatively high, indicating that Pliocene sediments are potentially a major sink for heavy metals characterized by high mobility and bioavailability. Fe-Mn oxyhydroxide phase is the most important fraction among labile fractions and represents 22% for Cd, 20% for Fe, 11% for Zn, 8% for Cu, 5% for Pb, and 3% for Mn. The organic matter-bound fraction contains 80% of Mn, 72% of Cu, 68% of Zn, 60% of Fe, 35% of Pb, and 30% of Cd (as mean). Summarizing the sequential extraction, a very good immobilization of the heavy metals by the organic matter-bound fraction is followed by the carbonate-exchangeable-bound fraction. The mobility of the Cd metal in the active and Fe-Mn oxyhydroxide phases is the highest, while the Mn metal had the lowest mobility.