In this paper, the seeping water and the sediments of the dam base in Fushui Reservoir, whose surrounding strata are mainly Silurian shale, were analyzed and investigated. The sediments are rich in Fe2O3 together with small amount of Al2O3 and SiO2. IR, XRD, SEM and TEM analyses show that crystalline minerals in the iron hydroxide sediments are mainly weakly-crystallized goethite with small amounts of illite and montmorillonite. There are some microtubular and spiral goethites scattered among the iron hydroxide colloidal cloud and submicrometer-size colloidal particles. The microtubular walls are found under TEM composed of nano-crystallines of goethite, and microspiral minerals are shown to have a resemblance to Gallionella bacteria in both morphology and size. It is obvious that they are closely related to microorganism mineralization.