The geochemistry of metals in the harbor and coastal zone of the town of Mytilene (island of Lesvos, Aegean Sea, Greece) was studied after normalization of the metal data to a conservative element. In the study area, Li was proven to be better suited than Al for such normalization and it was able to describe successfully the natural metal variability of the coastal sediments. Metal contamination (Cd, Cu, Pb, Zn) was recorded in the harbor sediments, while no pollution signs were detected in the wider coastal zone or the sediments of the ancient harbor, at the northern part of the town. The geochemical normalization of metal data to Li is a method that can detect the degree of metal contamination taking into consideration the natural metal variability in the sediments of a study area.