The park has the following popular fishing spots: St. Elias Lake, Mush Lake, Kathleen Lake, and Bates Lake. In Sockeye Lake and the creek that runs between Sockeye Lake and Louise Lake, fishing is not allowed. A territorial license is required for fishing in areas outside of park boundaries. Anglers are drawn to fish like rainbow trout, lake trout, and arctic grayling. Be certain to release any Kokanee that you catch because the Kokanee fishery in Kluane National Park and Reserve is closed.

This river, which runs through the Southwest Yukon, can be found near Haines Junction and at two locations on the Haines Highway. Whitefish, lake trout, and arctic grayling all use three shallow lakes just east of here; Crescent, Rainbow, and Lower Kathleen lakes At the end of September, the species of interest are Arctic grayling and spawning lake trout. The Kathleen River is where kokanee salmon are most frequently observed. In this river, only single-pointed barbless hooks are permitted. For northern pike, lake trout, and arctic grayling, there are catch and possession limits in place; Release of all rainbow trout is required.