Field observation on water quality and sediment properties was performed in Yokohama Port of Tokyo Bay in the winter of 2006. We developed an inexpensive method to determine the mud layer thickness efficiently using a cone penetrometer, which method would be a powerful tool to cover the spatial fluctuations of sediment properties as well as to be easily performed by citizens interested in estuarine environmental issues. We obtained detailed spatial variation in sediment quality and made discussion on the causes of its formation. We also found out the waters where high concentraions of sulfide were observed even in winter. The mechanism of the appearance of these polluted waters were attributed to the dredged bottom topography with slack waters, which situation seems to be the result of inappropriate dredging works. In shallower waters with the depth of around 5m, significant amount of benthic animals were observed. This indicates the importance of the conservation and restoration of shallow waters even in a busy port.