The west side of the bay consists of a 26,000 feet thick sequence of Paleozoic sedimentary rocks, mainly massive limestones and argillite. The oldest rocks in this sequence are the Late Silurian Willoughby limestone and the youngest being the Middle Devonian Black Cap limestone. An outcrop west of Tidal Inlet includes a sandstone, graywacke and limestone of unknown age. Sedimentary rocks of unknown age on the east side of Muir Inlet include tuff interbedded with limestone. The rocks exposed on the 1,205 foot high hill called “The Nunatak” have been metamorphosed. Early Cretaceous diorite stocks are exposed south of Tidal Inlet, and on Sebree and Sturgress Islands. Quartz diorite outcrops on Lemesurier Island. A granitic stock is exposed in Dundas Bay. Mafic dikes up to 20 feet in width occur throughout the area.
Glacial advances occurred 7,000, 5,000 and 500 years ago, with the last extending to the entrance of the bay, where it left a huge semicircular terminal moraine. The consequent surface glacial deposits include gravels as outwash and moraines. Glacial gravels extend up to 2000 feet up the mountain slopes. Lakes have formed where the glaciers have dammed the heads of valleys. Preglacial forests are found east of Goose Cove and on the east side of Muir Inlet. According to Rossman, “One of the outstanding features of the Glacier Bay area is the rapid advance and retreat of the glaciers during several substages within the last few thousand years.
The region experiences tectonic activity with frequent earthquakes. Earthquake-induced landslides have been significant forces for change, inducing tsunamis. Additionally, parts of the region are undergoing post-glacial rebound (also known as isostatic rebound), the process in which land rises after the weight of the glacier has been removed.