It is believed that in its earliest formation, over 50 million years ago, the Housatonic River was a straight flowing river, originating above the Hudson Valley in New York state. The forces of erosion caused the Hudson River to eventually break through and steal the headwaters of the Housatonic, leaving it with its source as it presently is, originating in Massachusetts.
The basin geology is somewhat complex, reflecting the results of hundreds of millions of years of natural events and processes. Most of the valley is underlain by metamorphic rock, mainly gneiss and schist from the Precambian era. This metamorphic bedrock was formed during the ancient collision of the North American continent with Europe and Africa some 300 to 400 million years ago. The intense pressure of the collision hardened the rock and caused it to fold and fault. These rocks form the steep mountains found in the valley.
Some portions of the valley, notably north of Falls Village, south of Cornwall Bridge and near New Milford are underlain by marble and are known as the "Marble Valley". During the Paleozoic era, seas covered a large portion of the valley, leaving sedimentary rock made up of carbonate mud, shells and marine fossils, material which later formed limestone. Metamorphism turned this limestone to marble. Above the bedrock is found glacial drift, comprised of the sand, silt and boulders left spread across the land by the melting glaciers as they receded over 18,000 years ago. As the glaciers advanced and receded, the river's path was continually altered, especially through the easily eroded Marble Valley.
Today the Housatonic River begins its journey in Massachusetts, separating the Taconic Mountain and New England Upland sections of the New England Physiographic Province. As it enters Connecticut's Western Uplands, it follows the Northern Marble Valley as far south as the Housatonic Highlands Plateau, two miles south of Falls Village. Here the river leaves the Marble Valley, flowing through the Housatonic Highlands until it rejoins the Northern Marble Valley at Cornwall Bridge, following it until it reaches Gaylordsville.
The river then cuts a gorge through the Hudson Highlands Plateau until it reaches the Southern Marble Valley north of New Milford center. Two miles south of New Milford, the river crosses Cameron's Line and enters the Southwest Hills, flowing south easterly until it eventually reaches the Coastal Slope and discharges into Long Island Sound.