This data is the first comprehensive baseline data on the geochemical composition of soil and sediments along the Nile River and Delta in Egypt that was subjected and analyzed by instrumental neutron activation analysis INAA. These data supported the research articles that were done to evaluate the elemental compositions and pollution sources in 176 sampling locations through 133 soil and 43 sediments samples along the Egyptian section of the Nile River and Delta - Egypt. "Geochemistry of sediments and surface soils from the Nile delta and lower Nile valley studied by epithermal neutron activation analysis" Arafa [1], "Major and trace element distribution in soil and sediments from the Egyptian central Nile valley" Badawy [2], and "Assessment of industrial contamination of agricultural soil adjacent to Sadat city, Egypt" Badawy [3]. The samples were analyzed by means of instrumental neutron activation analysis INAA and the concentrations in mg/kg of 28 major and trace elements are obtained. The quality control of the analytical measurements was carried out using different certified reference materials. Multivariate statistical analyses were applied. A total of eight individual and complex pollution indices were calculated in terms of the quantification of pollution extent and selection of the proper index based on the method and purpose of calculations. The spatial distribution of pollution load index PLI was mapped using GIS-technology. The normalized concentrations of the determined elements show no significant difference between soil and sediments concentrations and this, however, may be explained by the fact that origin of soil mainly is the sediments. To a clear extent, the concentrations of Ti (8017, 9672 mg/kg), V (124, 143 mg/kg), Cr (126, 160 mg/kg), and Zr (296, 318 mg/kg) are observed to be high in soil and sediments, respectively relative to other elements. Zr/Sc ratio shows a reduced sedimentary recycling and this may be explained by the tremendous influence of Aswan High Dam in preventing sediments supply from Ethiopian Highlights. Eventually, the pollution indices prove their suitability for assessing the individual and integrative contamination and show that there is no overall contamination. However, there are some contaminated localities mainly in Delta and mostly due to the dense population and anthropogenic activities. The data can be used as a raw data for constructing the first ecological atlas and evaluation of the ecological situation in terms of geochemistry and pollution.