Bonded warehouse are places were foreign imports can be stored or manipulated without the payment of duty or taxes. The government only gets a piece of the action (duty) if and when the goods are sold domestically.  Under the watchful eyes of Custom officers, it is the bonded facilities’ responsibility to protect the government's interest.

• F.E. Pinto's Pinto's Stores. Buildings #9, 10, 11, 16, 23, 24, 25, 26, 27, 28, 29, and 30 north pier, Atlantic Dock (Class 3)

• William Tobin's Tobin's Stores. Buildings #38, 40, 42, 44, 46, 48, and 50 north pier, Atlantic Dock; #54, 56, 58, 60, 62, 66 and 68 south pier, Atlantic Dock (Class 3)

• R. H. Laimbeer & Co.'s Laimbeer's Stores Buildings #6 and 9 Atlantic Dock (Class 3)

• Woodruff & Robinson's Woodruff & Robinson's Stores Buildings #42, 49 Commercial Wharf (Class 3)

• George E. Archer's Archer's Warehouse at Red Hook Point (Class 4)

• A. E. Lewis's Andes Stores at Red Hook Point (Class 4)

• Woodruff & Robinson's Erie Basin Stores. Buildings #5, 9 and 10 Erie Basin (Class 3) Yard, Erie Basin (Class 4) 

• J. W. Croxon's Clinton Stores.  Building #1 (Class 3), Yard (Class 4) foot of Ewen Street

• H. H. Durkee's Commercial Wharf. Buildings #38 and 39 (Class 3)

Class 3 bonded warehouses had to be used exclusively for the storage of imported goods.  At least one Customs officer was in charge of each building.

Class 4 bonded yards were required to be enclosed with a substantial fence at least 12 feet tall with a gate securable by a US Custom Service's lock.  These yards typically stored  wood, coal, mahogany, dye woods, lumber, molasses, sugar in hogsheads and tierces, railroad, pig and bar iron, anchors and chain cables.