Soil-plant systems play an important role in sand fixing and surface protection in the arid desert of China. This study examines the ecohydrological responses after a soil-plant system change for mobile dune stabilization by using a series of soil hydrological experiments and ecological investigation. The study results showed that decades of succession of soil-plant system has endangered the stability of the protection system. With the accumulated water and nutrient, a biological system develops in a thinner and thinner surface soil. Redistribution of precipitation has changed completely in the ecosystem. In 3–15 mm of soil, a high capacity of crust water retention ultimately limits most rainfall from infiltrating below 10–20 cm deep. When that takes place, lower plants begin to compete for water with grasses and shrubs. A drought horizon forms in 20–500 cm depth with shrub transpiration. Artificial shrubs with deep roots obtain hardly rainfall supply and are gradually eliminated from the protection system. All changes in water environment affect the structure and function and stabilization of whole protection systems. It is necessary to establish a relatively stable water environment by managing the soil-plant system for constructing a sustainable protective system in arid desert.