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Precise knowledge of the soil organic carbon (SOC) stocks under various land uses is needed to meet the Kyoto Protocol and for the sustainability of natural resources. The purpose of the present study was to (1) gauge the depth and spatial distribution of the soil bulk density (BD), soil organic carbon (OC) stocks, and soil organic matter (OM) among the various land uses in the northern Nile Delta in Egypt; (2) estimate the soil carbon sequestration rate (CSR) under different land uses in the region; and (3) establish baseline data for SOC stocks in future studies on the dynamics of SOC. The study area was divided into ten sampling zones to represent each land use in the northern Nile Delta. Each sampling zone was further divided into four sampling sites to represent virgin lands and fish farms, and twelve sites were used to represent three crop types and four cultivation histories. The crops included clover, (Trifolium alexandrinum L.), sugar beet (Beta vulgaris L.), and rice, (Oryza sativa L.) and the years spanned were 5, 15, 30 and 50. The effects of the crop type on the SBD, SOC content, and SOC stocks were significant. In general, the SOC stocks increase as the number of years of cultivation increased. Thematic maps were produced using Geographical Information Systems (GIS) mapping. The Inverse Distance Weighted (IDW) technique in ArcGIS10.4 software revealed that the spatial pattern of the SBD, OC content, and stocks conformed to the soil analysis results. The SOC stocks of the croplands and fish farms were 1.6 and 1.5 times higher, respectively, compared to those of virgin land. Rice cropland had the lowest SBD (1.34 g cm−3) and the highest OC stocks (7.46 g C kg−1). The conversion of virgin land into croplands or fish farms actively contributed to the carbon storage rate (CSR).