Dredging and Waterway Modification
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Each year, an estimated 4,000 commercial ocean-going vessels move through the San Francisco Estuary carrying more than 75 million tons of cargo worth approximately $20 to $25 billion. These vessels depend on deepwater ports and shipping channels in the Bay and Delta that must be dredged each year to maintain their navigability. (The total volume of material dredged annually from channels, ports, and marinas in the Estuary has decreased from approximately eight million cubic yards (mcy) in 1993 to just over four million cubic yards as of 2006.) Historically, dredged material from navigation channels was disposed of at various locations in the Bay. In the 1980s, concerns about impacts to the Estuary's water quality and aquatic life from dredging (and disposing of dredged material in the Estuary) highlighted the need for improved management of and alternative disposal options for dredged material.

Another related issue is the potential for a sediment debt in the Estuary. Due to a variety of factors, such as an increase in water diversions upstream of the Delta and morphologic and hydrologic alterations to the major tributaries and rivers that transport sediment into San Francisco Bay, the Estuary may be receiving less sediment than it did in the past. Less sediment could impede wetland formation and lead to increased erosion of existing habitats. Adequate sediment input into the Estuary will be increasingly important as the rate of sea level rise continues to accelerate, and storms become more intense. An adaptive, collaborative sediment management approach that considers all aspects of Bay sediment dynamics will be critical in addressing the impacts of global climate change and other human-induced changes in Bay sediment dynamics.