This paper investigates the interplay of the hydrogeological characteristics, soil properties and recent land reclamation projects on the distribution of waterlogging and salinization within the Farafra Oasis. The multi-temporal remote sensing data and field observations show that new reclaimed areas have been recently cultivated in distant areas from the old agricultural land. These new cultivations have developed widespread waterlogging, seepage channels and soil salinization. Analyses of the Shuttle Radar Topography Mission digital elevation model (DEM) showed that both old and new agricultural areas are located within same closed drainage basin. The fluvial channels of these catchments, which were developed during wet climatic pluvial, have largely been obliterated by the prevailing aridity and often buried under aeolian deposits. However, the new cultivations have been developed on the fingertips of these fluvial channels, while the old fields occupy the low-level playas. The soil of the new cultivated areas is mainly lithic with a high calcium carbonate content, thus limiting the downward percolation of excess irrigation water and therefore developing perched water table and seepage through the palaeo-channels. The automatically extracted drainage networks from DEM resemble fluvial patterns and coincide with the seepage channels slowly heading toward old cultivation. The inactive alluvial channels and landforms have to be considered when planning for new cultivation in dryland catchments to better control waterlogging and salinization hazard. It is highly recommended that newly developed seepage channels have to be detected and intercepted before reaching old agriculture areas. Therefore, the ‘dry-drainage’ concept can be implemented as the seepage water can be conveyed into nearby playas reserved for evaporation. Copyright © 2012 John Wiley & Sons, Ltd.