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Determination of chemical elements, Al, Cd, Co, Cr, Cu, Fe, Li, Mn, Mo, Ni, P, Pb, Sc, Sr, Ti, Y, and Zn have been performed in agricultural and desert soils and alfalfa (Medicago sativa) at Aswan area. Consequently, the pollution indices, univariate and multivariate statistical methods have been applied, in order to assess the geochemical characteristics of these elements and their impact on soil environmental quality and plant, and to reach for their potential input sources. The investigation revealed that the mean and range values of all element concentrations in agricultural soil are higher than those in desert soil. Furthermore, the agricultural soil displayed various degrees of enrichment and pollution of Cd, Zn, Mo, Co, P. Ti, Pb. The geochemical pattern of integrated pollution indices gave a clear image of extreme and strong pollution in the agricultural soil stations, their poor quality with high risk to human health and considered as a tocsin for an alert. In contrast, the desert soil is the good environmental quality and safe for plant, animal and human health. Alfalfa is tolerant plant and considered as a biomarker for P and Mo in polluted agricultural soil. Four geochemical associations of analyzing elements in agricultural soil and three ones in desert soil have been generated, and their enhancements were essentially caused by various anthropogenic activities and geogenic sources. The investigation also revealed that the broad extended desert soil is fruitful and promising as cultivable lands for agricultural processes in the futures. (C) 2015 Elsevier Ltd. All rights reserved.