The Isles of Shoals comprise a small archipelago that straddles the New Hampshire/Maine border about 5 miles off the coast. Star Island, Lunging Island, and White and Seavey Islands are the major islands in New Hampshire but are surrounded by plentiful small ledges. Like many islands off the coast, these can be very productive as migrant traps in spring and fall. Water birds are also plentiful around the islands year-round.

Jeffreys Ledge, a large glacial remnant, is located ~35 km off the New Hampshire coast. It is a long (60 km), linear bank extending from Cape Ann, Massachusetts to Cape Elizabeth, Maine. Typical of glaciated features, the shallower regions of Jeffreys Ledge (~50-75 m) are composed of coarse sediments (mostly gravels with numerous cobble and boulder fields). Adjacent to Jeffreys Ledge are muddy basins that are over 200 meters in depth.

Historically, Jeffreys Ledge has been an important fishing ground of the Gulf of Maine with high yields of cod, haddock, hake, and flounder. However, in 1998, the Western Gulf Of Maine Closure Area was established by New England Fisheries Management Council, closing a large area of Jeffreys Ledge to ground fishing in hopes of restoring stocks.

In 2002, the University of New Hampshire initiated an interdisciplinary study of Jeffreys Ledge in order to better understand the physical and biological processes influencing this important ecosystem and to evaluate the effects of the closure.

The New Hampshire Coastal Waters extend from New Castle on the border with Maine to Seabrook on the border with Massachusetts.