The subtidal portions of the estuary keep flowing even when the tide is all the way out. The deepest sections of these are the channels.
The bottom of subtidal areas in the lower part of Great Bay Estuary are mostly rock and cobble, with sand to sand/mud closer to shore. In the upper estuary the bottoms are mostly sandy mud and silt, with harder substrate in the channels.
The importance of this particular habitat is not understood as well as other habitats in the estuary, according to Fred Short, a research professor of natural resources at the University of New Hampshire. In The Ecology of the Great Bay Estuary, Short writes that the subtidal area is thought to be a place where fish and invertebrates retreat at low tide. Additional habitats can be found in some of these subtidal areas in the form of oyster and eelgrass beds.
Due to extremely strong, erratic currents and sinking mud in many parts of the estuary, it appears very unsafe to snorkel around in search of subtidal creatures in many places. If you are determined to find them, contact a local dive shop to see about training and connections to experienced guides for the safest possible expedition.
Some protected areas are good for snorkeling. One is at the end of Ordiorne Point, upstream from the jetty along the areas of rocky shore beyond the sandy beach.
Another way to explore this habitat is to take part in one of the UNH Discovery Cruises of Great Bay. These day-long trips up the estuary include a netting of some subtidal algae and animals.
A channel flow pattern can be a visually interesting part of the landscape. During low tide, some scenic overlooks offer good views. Try hiking the rocky shoreline around the south end of Adams Point in Durham, at Great Bay. The channel passes between the point and the Footman Islands.
Sagamore Creek dwindles to a trickle, but it still leaves a nice channel pattern. You can see it from the Sagamore Creek overlook at the end of the self-guided forestry trail at the Urban Forestry Center, in Portsmouth.