The soft clays, alluvial deposits, are widely distributed over several coastal regions in Japan. The inferiority of these kinds of soils is the main obstacle for using them as construction and foundation materials. Furthermore, the inferior clay soils floating and accumulating on the sea bed, the so-called“Hedoro”, disturb the navigation and decrease the ability of port functions. Thus, in recent years a very difficult social problem of coastal pollution has arisen. The purpose of this study was to investigate the influences of microorganisms on engineering properties of soft clays in order to solve the above problems as well as to use them as engineering materials, such as in reclamation work and embankments. The growth of microorganisms was obtained by adding trace amounts of microbial nutrients and inocula into the clay soils and the properties of these treated soils were improved.