The Central Fergana region is one of the overpopulated regions of Central Asia, which includes parts of Uzbekistan, Kyrgyzstan, and Tajikistan. Here, in the dry subtropical climate are the most ancient, irrigated oases used for agriculture. Fergana valley is the key to the food security of the region as a whole. The article provides information on diversity and chemical composition of newly developed, new and old-irrigated Calcisols soils formed on alluvial and alluvial–prolluvial sediments. Soils are poor with organic matter (0.37–0.81% of organic carbon), with high nitrogen content (C/N ratio is 4.92–5.79), and with neutral (7.01–7.30) pH values. Data on the content and the ratio of the key components of soil salinity (Na2CO3, Ca(HCO3)2, CaSO4, MgSO4, Na2SO4, NaCl) and the bulk content of salts in soils under different irrigation regimes are presented. It was shown that Na2CO3 concentration is minimal in all the soils, and this salt presents only in ground waters (0.100–0.135 g L−1). Newly irrigated soils are characterized by higher content of salts than old irrigated soils. All the soils investigated are characterized by increasing salinity rate within the soil depth with the highest content of all salts in ground waters. This chloride–sulfate type of salinization is most pronounced in all the soils studied. Gypsum content in agricultural soils results in limited water and nutrient retention and the potential for dissolution, primarily in response to irrigation. The soils of the Fergana Valley are also subjected to polychemical pollution, so the content of trace elements in them was studied. Irrigated meadow-takyr and meadow-saz soils show low levels of environmental hazard, but irrigation results in accumulation of such trace elements as nickel (30 mg kg−1), arsenic (11.75 mg kg−1), bromine (5.00 mg kg−1), antimony (1.48 mg kg−1), cesium (5.00 mg kg−1), and hafnium (2.97 mg kg−1). Irrigation also affects the soil texture and thus increases fine particle percentages in the superficial soil horizons. Thus, the complex chemical characteristics of salinized soils are presented for numerous irrigated landscapes of the region.