Silicon is a necessary nutrient for diatoms, silicon uptake in diatom reproduction decreased seawater silicon content. This paper clarified the characteristics of silicon transferring in the sea, which plays an important role in phytoplankton growth, zooplankton graze and marine ecosystem. Analysis revealed that silicate is supplied by terrestrial sources, through plankton uptake, death, and eventually deposits to the sea bottom, and cannot diffuse upward. This is a general silicon deficit process. Many global marine waters showed the same silicon transfer route: land→silicon biogeochemical process→sea bottom. River flow brings abundant silicate into marine waters, silicate concentration in the waters decreased in the distance away from the river estuaries. In discussion of silicon characteristics and its transfer route, it was considered that the main factor controlling the mechanism of diatom and non-diatom red tides occurrence is silicon, and the changes in silicon source. Human activities, such as sea-route cutting by building embankment and dam, and silicon supplement by the sea, such as sandstorm, rainstorm and storm tide, have largely impaired the earth ecosystem and hugely threatened the human existence. It is suggested in this paper that man should resume the original face of the Si input into the sea to keep natural ecosystem in sustainable pattern.