Afforestation has been conducted for preventing desertification in the depleted Aral Sea bed. The present study aimed to investigate the effects of vegetation establishment on changes in soil properties and enzyme activities. In August 2017, soil samples from degraded area (DA), areas afforested in 2002 (P1) and 2013 (P2), and natural vegetation area (NA) in the northern part of the Aral Sea bed were analyzed for soil water content (SWC), pH, salinity, total N and organic C concentrations, exchangeable cation concentrations (K⁺, Mg²⁺, Ca²⁺, and Na⁺), and cation exchange capacity. Also, enzyme activities were analyzed for the topsoil up to a depth of 10 cm. The changes of soil chemical characteristics were distinct in P1 and NA compared with DA, and no significant difference was found between P1 and NA. Our findings indicate that vegetation establishment increased soil organic matter which is strongly associated with SWC, organic C concentration, and overall soil fertility. Moreover, soil enzyme activities increased with SWC and total N and organic C concentrations in both vegetated areas (P1 and NA). It seems that the effects of vegetation establishment on soil amelioration are similar in long-term plantation and natural vegetation areas.