Lower Bay
- Ambrose Channel
- Swash Channel
- Sandy Hook Channel
- Terminal Channel
- Atlantic Highland Anchorage
- Chapel Hill South Channel
- Coney Island Channel
- Rockaway Inlet
- Gravesend Bay Anchorage
- Raritan Bay East Reach
Raritan Bay
- Raritan Bay West Reach
- Seguine Point Bend
- Red Bank Reach
- Ward Point Bend (East & West)
- Raritan River Cutoff
- Perth Amboy Anchorage
- South Amboy Reach
- Ward Point Secondary Channel
- Great Beds Reach
Jamaica Bay
- Runway Channel
- Island Channel
- Beach Channel
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Arthur Kill
- Outerbridge Reach
- Port Socony Reach
- Port Reading Reach
- Fresh Kills Reach
- Tremley Point Reach
- Pralls Island Reach
- Gulfport Reach
- Elizabeth Port Reach
- South of Shooters Island Reach
Newark Bay
- North of Shooters Island Reach
- Newark Bay South Reach
- Newark Bay Middle Reach
- Newark Bay North Reach
- Port Newark Branch Channel
- Port Newark Pierhead Channel
- Elizabeth Channel
- South Elizabeth Channel
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Kill van Kull
- Bergen East Point Reach
- Bergen West Point Reach
- Constable Hook Reach
Upper Bay
- Pierhead Channel
- Anchorage Channel
- Red Hook Channel
- Red Hook Flats Anchorage
- Bayridge Channel
- Greenville Channel
- Claremont Terminal Channel
- Buttermilk Channel
Hudson River
- Weehawken Edgewater Channel
East River
- East Channel
- West Channel
- South Brother Channel
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