Water resources within Wrangell-St. Elias include wetlands, deep-water habitat and coastal systems. Six major river systems originate within the park and the lowlands are dotted with lakes and bogs. Major salmon runs occur in the Copper River and tributary streams. Rivers are one focus of recreational and subsistence use and when frozen become primary routes for winter access.
Three million acres of the park are Palustrine (marsh-like) characterized by lush nonvascular plant communities and abundant aquatic invertebrates. There are over 46,000 acres of natural lakes including six large lakes and over 500 small ponds and lakes (under 1000 acres in size each). Water issues are controlled in part by the extreme winter weather. Five different types of permafrost occur commonly throughout the park that significant change surface water dynamics. Ice flows and periodic ice jams can cause brief but sometimes catastrophic flooding in low-lying areas. Deeply frozen ponds limit the distribution of some species of fresh water fishes and amphibians are extremely rare within the park in part due to the extreme temperatures.