Its lower portion is a complex island estuary with connections to the Kennebec River downstream of Merrymeeting Bay.

The West Branch Sheepscot River joins the main stem between Cooper's Mills and North Whitefield.

Sheepscot Bay is navigable for a distance of approximately 15 miles (24 km) from Wiscasset to the mouth between Reid State Park and Southport Island.

In the Summer/Fall of 2019 the Head Tide Dam near Alna was partially breached to allow easier passage for differing fish species.

Alewives, herring, Atlantic salmon, and resident trout species will assuredly benefit from these restoration efforts.