Most of the lakes in the park were created thousands of years ago. As the glaciers moved they pushed aside soil and dug into the ground. When the glaciers melted they left behind an indentation in the ground that filled with water from the melting glacial ice. These became the lakes that we see today. Jackson Lake, the park's largest lake, is a natural lake that has been altered by a human-made dam.

Ponds can be formed like lakes but may also be the result of part of a river being blocked, beavers building a dam, natural sinkholes in the ground, or even human activity. The plant and animal life in a pond area is very diverse and productive.

Ponds and lakes provide a variety of habitat in and around them. From cutthroat trout to crawfish, from great blue herons to moose, almost all wildlife in the park derive some benefit from lakes and ponds. Ponds and lakes also provide recreational opportunities for visitors. Some of the easiest and most popular hikes are around lakes and ponds. All of the lakes are open to swimming and non-motorized boating. Jackson Lake also allows motorized boats for recreational use.