During the construction period of sea-crossing bridge, pile foundation construction and other operations are easy to cause marine water environment pollution. In order to enhance the green development level of the cross-river (sea) channel project, this paper selects the Shenzhen-Zhongshan Link, a typical cross-sea traffic cluster project, as the research object. And introduces water environmental protection technologies such as bored pile with steel casing, cofferdam formed by locking steel pipe pile, cofferdam formed by geotech-bag, and whole trestle across the sea. The variation characteristics of suspended solids, oil, inorganic nitrogen, inorganic phosphorus and heavy metal concentrations with respect to time and space in the whole sea area of the bridge project were systematically analyzed, to explore the influence of bridge construction on water quality of the whole sea area. Further verify the application effect of the water environmental protection technologies, and provide reference for similar bridge green construction and water environment protection research in the future.