The western shore of Nottawasaga Bay is determined by the Niagara Escarpment, which reaches Nottawasaga Bay between Thornbury and Meaford. The southern shore is flat limestone plain, with cedar marshes. The Nottawasaga River flows into Georgian Bay near the southern end of the bay, and from the estuary onward to the east the shore is predominantly sand dunes and marshes created by the strong predominant northwest winds. This part of Nottawasaga Bay is heavily built up with summer homes.
Nottawasaga Bay is one of Ontario's busiest tourism areas, but recreational use has taken a toll on it. Pollution from cottages, towns, industry and agriculture have caused a noticeable decline in water quality in recent years, resulting in some beach closings.