The Fergana valley is a region critically important for food safety in Central Asia. The human-altered soils in Fergana are considered a key component of the transboundary region between sub-boreal and sub-tropic climatic zones. As the results of the investigation of irrigated chloride-sulfate saline soils near the surface showed the deep petrocalcic and petrosalic horizons at various depths with extremely low water and air permeability. The chemical, pedogeochemical, and biogeochemical properties of soils, the content of macroelements, trace elements, lanthanides and radionuclides, and the general geochemical characteristics of desert zone soils were investigated and determined. The background contents of the mentioned elements were recognized. The irragic, salic, gleyic, and gypsic horizons in soils were identified by WRB 2015. They can be used as reference horizons for biogeochemical studies and soil management activities. The irragic, gleyic, carbonate-gypsum horizons, evaporation, oxygenic, and other geochemical barriers were studied and revealed. The processes of accumulation, migration, and differentiation of chemical elements in solum as well as in parent materials occur with the joint effects of exogenous, endopedogenic, and artificial factors. These fluxes of elements, in turn, are affected by the nature of soils and parent materials. In this process, unexplored elements form only scattering fluxes. During the vegetation season, as well as the leaching period, considering the various horizons features will help to save significant amounts of irrigation water.