Agriculture in Central Asia and in the Fergana Valley in general strongly depends on irrigation and drainage of agricultural lands. The Fergana Valley includes about 45% of the irrigated area in the Syr Darya River basin. Active use of irrigation in agriculture can lead to changes in the soil’s natural composition, as well as pollution and changes in the soil’s physical and chemical properties. Soil degradation in the process of irrigation can lead to a decrease in crop yields and, as a consequence, to a decrease in food security in the region. In this study, a comparative analysis of three main types of Calcisols (Dark, Light, and Typical) before (uncultivated soil) and after agricultural use (surface-irrigated agricultural soil) was carried out. Irrigation leads to increment of SOC stocks in Typical (from 113.8 to 126.3 t/ha) and Light (from 62.8 to 100.1 t/ha) Calcisols and to decreasing of SOC stocks in Dark Calcisols (from 160.1 to 175.3 t/ha). In general, the content of biophilic elements (SOC and TN) is lower in irrigated soils, and their distribution in the soil profile is close to the functional relationship (r2 0.98 to 0.99). In uncultivated Calcisols, the profile distribution of SOC and TN is more heterogeneous (r2 0.67 to 0.97). Changes in the humification processes of soil organic matter are also identified; in soils after irrigation the carbon ratio of humic/fulvic acids (CHA/CFA) is lower (<1) compared to their uncultivated counterparts (~1). The alteration of the soil water regime also resulted in transformation of the individual compositions of amino acids. All studied types of Calcisols are characterized by changes in particle-size distribution of soils especially in the number of the silt fraction (0.01–0.05 mm) and the difference between uncultivated and irrigated soils, 10–20%, which is associated with the processes of colmatage by accumulation of a fine fraction and replacement of sub-fractions in the fraction of sand. The highest concentrations of nutrients are characteristic of the upper soil horizons (P up to 231, K up to 2350 mg/kg), which indicate their pedogenic and agrogenic origins rather than inheritance from the parent material. Soil P and K availability is rather high, with non-labile forms prevailing, although of near reserve. The surface irrigation results in apparent accumulation of water-soluble Mg2+ (1.6–2.1 meq/100 g) and K+ (0.6–0.9 meq/100 g), but the cation of Ca2+ predominates in the base cations’ composition, which is the most favorable in terms of soil agrogenic property formation. Data obtained will be useful for development of strategies for effective land use in arid, subtropical, overpopulated regions of Central Asia that have deficient water sources and intensive soil degradation.