The large amount of tidal freshwater riverine habitat found in the Kennebec/Sheepscot Rivers' estuaries makes this system unique in the State of Maine. There is a total of 11,140 acres of tidal riverine habitat in this system with most of it being above the outlet of Merrymeeting Bay (Table 6). This represents 84% of the total tidal riverine habitat found in the State of Maine north of Cape Elizabeth.18 This subsystem can be further divided into classes of types of habitat, such as open water, nonpersistent emergent wetland, flats, and beach/bar (Table 6). There are 5,682 acres of open water habitat in this subsystem which represent 80% of this type of habitat in Maine north of Cape Elizabeth. There are 3,133 acres of nonpersistent emergent wetland which represent 98% of that found above Cape Elizabeth. This tidal riverine section constitutes one of the most important spawning and nursery areas for anadromous fish north of the Hudson River.
The Kennebec River estuary below Chops Point (outlet of Merrymeeting Bay) forms a complex with that of the Sheepscot River estuary. Less saline surface water from the Kennebec River flows through the Sasanoa River into Hockomock Bay on an outgoing tide, whereas highly saline water from the Sheepscot River enters Hockomock Bay through Goose Rock passage on the incoming tide as bottom water in the Sasanoa. Water is also exchanged in Montsweag Bay between Hockomock Bay and the Sheepscot River in Wiscasset. Thus, both Hockomock and Montsweag Bays act as mixing basins for the Kennebec and Sheepscot Rivers' water, with there being an indirect exchange between the two systems.19 Hockomock Bay is also connected with the Kennebec River through Back River, which is very shallow near Hockomock Bay. The dynamics of water exchanged between the two systems and the exact influence one river system exerts upon the other has not been extensively studied.