Johns Hopkins Glacier starts at an elevation of about 8,000 feet (2,438 m) on the eastern flank of Mount Lituya in the Fairweather Range of the Saint Elias Mountains and flows generally east-northeast for 13 miles (21 km) to the head of Johns Hopkins Inlet in Glacier Bay National Park and Preserve, about 104 miles (167 km) southeast of Yakutat and 58 miles (93 km) northwest of Gustavus, Alaska. In 1893, the terminus of what was originally named Grand Pacific Glacier by Harry F. Reid was 14 miles (23 km) farther west situated between Reid Glacier and Russell Island in Reid Inlet. The glacier retreated and separated into two ice fronts exposing new fjords. The ice front to the north retained the name Grand Pacific Glacier and the new fjord was named Tarr Inlet by Lawrence Martin after Ralph S. Tarr, who was a professor of physical geography at Cornell University. The other newly exposed fjord to the west retained the name Reid Inlet and its ice front was named Johns Hopkins Glacier by William S. Cooper in 1931 after Johns Hopkins University in Baltimore, Maryland. With the further retreat of the Johns Hopkins Glacier to the west, and the gradual lengthening of Reid Inlet, the historical relationship to Reid Glacier became obscure and in 1954, the U.S. Board of Geographic Names changed the name from Reid Inlet to Johns Hopkins Inlet. In 1893, the retreating glacier terminus was exposing bedrock at the head of present-day Glacier Bay consisting mostly of an igneous rock called granodiorite that intruded into the Alexander terrane as magma during the Late Cretaceous. In the early decades of the 20th century, the glacier had retreated farther and was exposing sedimentary rocks of the Chugach terrane in Johns Hopkins Inlet that consisted mostly of sandstone and mudstone turbidites, and greywacke that had been intruded by magma during the Oligocene and Eocene creating plutons of granodiorite and quartz diorite. The Alexander terrane to the east is separated from the Chugach terrane by the Border Ranges Fault that is roughly aligned with the axis of Tarr Inlet. The Chugach terrane is separated from the Yakutat terrane to the west by the Fairweather Fault which is roughly aligned with Desolation Valley. These faults have created a shear zone resulting in considerable seismic activity and geological deformation.

There is regional archeological evidence of human settlement in Icy Strait and near the mouth of Glacier Bay but it cannot be conclusively determined who these prehistorical people were. Tlingit oral tradition tells of a village in Glacier Bay that they were forced to leave because of an encroaching ice front. Historical settlements are known from Dundas Bay, Bartlett Cove, and Excursion Inlet. In 1794, Lieutenant Joseph Whidbey, master of the HMS Discovery during the Vancouver Expedition of 1791–95, reported that his survey of the north shore of Icy Strait was blocked by a wall of ice 2 miles (3.2 km) wide. Vancouver claimed the land for Britain which conflicted with an earlier Russian claim from Yakutat. The issue was not resolved until the Treaty of Saint Petersburg in 1825 which favored the Russians. In 1867, the Alaska Purchase transferred the territory from Russia to the United States. By this time the glacier terminus in Icy Strait had retreated about 15 miles (24 km) revealing the entrance to Glacier Bay and present-day Bartlett Cove. In 1879, the naturalist John Muir recorded the ice front about 32 miles (51 km) from Icy Strait. In 1899, Edward H. Harriman financed an expedition to Alaska that visited Glacier Bay and discovered an uncharted fjord with many unnamed glaciers that were subsequently well documented. A dispute with Britain about the boundary location between Canada and the District of Alaska was resolved by arbitration in 1903. By 1916, the Grand Pacific Glacier which once filled Glacier Bay had retreated about 60 miles (97 km) from Icy Strait which represents one of the fastest known glacial retreats. Today, the glacier terminus is within 1 mile (1.6 km) of the Canadian border. In 1925, President Calvin Coolidge declared Glacier Bay a national monument after intense lobbying by Muir, Cooper, Harriman and many others. In 1939, another proclamation added additional land to the monument. In 1980, the Alaska National Interest Lands Conservation Act changed the designation to a national park with about 3.3 million acres (1.3 million ha) and added a preserve of 57,000 acres (23,067 ha).

Most of the glaciers in the Saint Elias Mountains are retreating but Johns Hopkins Glacier is one of the few advancing tidewater glaciers. The glacier is about 1 mile (1.6 km) wide, 250 feet (76 m) high at the terminus, and 200 feet (61 m) deep at the waterline. It is formed from numerous tributary glaciers, many of which extend 12 miles (19 km) or more into the surrounding peaks. About 50 medial moraines develop from the joining of these tributary glaciers. The debris in these moraines can be seen in the ice face and extending up the glacier as prominent dark bands. This debris is transported in and on the ice and released either by melting of the ice face or calving of icebergs into Johns Hopkins Inlet. Meltwater from the glacier is also discharged from submarine tunnels or conduits located near both the eastern and western edges of the glacier. Sometimes this water can be seen emerging at the inlet surface as turbulent roils or fountains. In the 1970s, Johns Hopkins Glacier flowed at a rate of about 3,000 feet (900 m) per year or about 8 feet (2.4 m) per day. The glacier front has advanced about 2 miles (3.2 km) since 1932 and has merged and separated with the Gilman Glacier at its eastern edge several times. The two glaciers were most recently attached in 2000 but since 2016 they are just barely separated. The rate of glacial advance and retreat is related to the concentration of icebergs calving from the glacier terminus. Hundreds of harbor seals haul out on these icebergs. During the month of June, the icebergs are used primarily by females and pups, and in August, by molting seals. The number of seals hauled out is correlated with the percentage of ice cover, and the number of icebergs suitable for hauling out may limit the abundance of seals in this area. The number of predators on harbor seals, such as killer whales, Steller sea lions, and sleeper sharks is therefore also affected indirectly by the number of icebergs. Read more here and here. Explore more of Johns Hopkins Glacier and Glacier Bay National Park and Preserve here: