The soil samples were collected in Xiaojiang River Basin at different altitudes from 2010?–?2011. The changes of soil physiochemical properties, including soil pH, organic matter, phosphorus and iron oxide, were studied to reveal the variation of water-level-fluctuating belt soil and its environmental impact. The results showed that: the soil pH, organic matter, available phosphorus(P), total P, amorphous iron(Feo), free iron (Fed) and clay content increased after flooding; the soil organic matter, available P, Feo, Fed and clay content decreased after drain; the Feo/Fed of soils decreased from Shuangjiang and Gaoyang sites in 170 m and 165 m altitudes under a “drain-flooding” cycle, but the Feo/Fed increased significantly by 12.4% and 94.5%, respectively, in 150 m altitude. As the physiochemical properties of soils changed obviously change under “drain-flooding” process and P accumulated, the increasing environmental risk should be taken into consideration seriously.