The study of atmospheric inputs to the sea has become a new focus of biogeochemical cycle in the past few years. Fluxes of atmospheric pollutants to the sea, the effects of atmospheric input on marine environment and ecosystem, and study projects on this point are reviewed. The atmospheric deposition fluxes/proportions of atmospheric versus riverine inputs of nutrients, aerosol, heavy metals and some persistent organic pollutants (POPs) are given. It is shown that the amount of nitrogen from atmosphere to the sea is about 20%~50% of the total input from atmosphere and rivers, and the atmospheric inputs of PAH, PCB, DDT and heavy metals, such as Pb, Cd, Cu, Fe are 50%~80% of the total inputs. The different effects of nutrients, such as nitrogen and phosphorus, heavy metals and POPs, such as PAH, PCBs and pesticides on marine environment and ecosystem are discussed. Nutrients, nitrogen and phosphorus from atmosphere deposition are important factor to enhance new primary production in open seas, but have some positive influence on the nutrificated coastal oceans. More and more species of POPs and heavy metals are detected in water and sediment in the sea, which may prevent the production of phytoplankton and change the natural structure of marine ecosystem.