The Great Bay Estuary begins at the mouth of the Piscataqua River. Tides carry salt water into the estuary twice daily from the Atlantic Ocean. Here it mingles with the fresh water influence from the various rivers that empty into Great Bay. New Hampshire has the shortest coastline of any state, but those 18 miles increase to 150 miles of tidal shoreline when the Great Bay Estuary is included. It is one of the largest estuaries on the Atlantic Coast and at 10 miles inland is one of the most recessed.

Approximately 14,000 years ago, following the melting of the glaciers, the Great Bay Estuary was formed. The glacial melt waters contributed to rising ocean waters, which flooded the land and filled the river valleys that make up Great Bay today.

There are five very different water dominated habitats that make up the Great Bay. In order of abundance they are: eelgrass meadows, mudflats, salt marsh, channel bottom, and rocky intertidal. These habitats are home to 162 bird, fish and plant species (23 of which are threatened or endangered), countless invertebrate species and even the occasional harbor seal.

Eelgrass is one of a very few underwater marine flowering plants. It has many functions in the estuarine system. The eelgrass community provides habitat for several organisms, especially the young of fish and invertebrates. Eelgrass roots help stabilize the bottom sediments. Eelgrass plants help maintain water quality and clarity by filtering the water allowing sediments to settle and then using the excess nutrients for growth.

More than half of Great Bay is exposed as mudflats at low tide. Worms, soft-shelled clams, mud snails, green crabs, wading birds, horseshoe crabs and many other animals utilize the extensive mudflat habitat for feeding, reproduction and protection from predators.

The channel bottom habitat provides a place for fish and invertebrates to move to at low tide. It is also the preferred habitat for oysters, a highly specialized animal that only live in estuaries.

Rocky intertidal habitat provides firm anchorage for seaweeds, barnacles, and ribbed mussels. Each winter, much of the standing crop of seaweeds becomes entrapped in ice. When the ice begins to break up in spring, the seaweeds are torn from the rocks and enter into the detrital cycle.