Miramichi Bay is separated into the "inner bay" and the "outer bay", with the division being a line of uninhabited barrier islands which are continually reshaped by ocean storms. The largest of these islands is the uninhabited Portage Island, which was broken in two during a violent storm in the 1950's. The islands provide some protection to the inner bay from ocean storms in the Gulf of St. Lawrence.
The Inner Miramichi Bay, and the lower portions of its tributary rivers (including the Miramichi River), are parts of a drowned river valley system. Since deglaciation, sea level rise in Miramichi Bay has flooded the mouths of these rivers with saltwater. The flooded, meandering, ancient Miramichi river channel forms a navigable route through the Inner Bay for ocean-going ships entering the port at Miramichi (formerly the ports of Chatham, New Brunswick and Newcastle, New Brunswick). The inner bay measures only 4 m deep on average, with the navigation channel measuring only 6-10 m. Since dredging maintenance of this channel has stopped, the port is now only accessible to ships with a shallow draft.