Most of the lake is protected by the Boundary Waters Canoe Area Wilderness in the United States and by Quetico Provincial Park and La Verendrye Provincial Park in Canada.

A small part of the lake's southern arm is outside the Boundary Waters.

Minnesota Department of Natural Resources has issued a consumption advisory for some fish in Saganaga Lake due to mercury pollution.

[1] The Lake is the eastern boundary of the historical Hunter Island region.

Historic Chik Wauk Lodge, now Chik-Wauk Museum and Nature Center, overlooks the lake.