The following list covers all the waterways (and a few major portages) along the AMVR. Highlighted text indicates sections based on geographic, or heritage regions easier reference.

The St. Lawrence - Ottawa Valley St. Lawrence River Ottawa River Nipissing Mattawa River La Vase Portages Lake Nipissing French River Great Lakes Georgian Bay - Lake Huron Lake Superior Hudson Bay Divide Grand Portage Pigeon River Boundary Waters/Quetico Pigeon River North, South Fowl Lake Moose Lake Vasuex lake Fan Lake Mountain Lake Watap Lake Rose Lake Rat Lake South Lake Height of Land portage North Lake Little North Lake Little Gunflint Lake Gunflint Lake Magnetic Lake Pine River Pine Lake Granite River Lake Saganaga Cypress Lake Knife Lake Knife River Carp Lake Birch Lake Basswood Lake Basswood River Crooked Lake Iron Lake Lac La Croix Loon Lake Loon River Little Vermilion Lake Vermilion Lake Namakan Lake Rainy Lake Rainy River Lake of the Woods

Winnipeg River/Lake Winnipeg Winnipeg River Gun Lake Little Sand Lake Roughrock Lake Tetu Lake Eaglenest Lake Numao Lake Nutimik Lake Dorthy Lake Natalie Lake Lac Du Bonnet Lake Winnipeg Lower Saskatchewan River Cedar Lake Saskatchewan River Sturgeon-Weir Region Cumberland Lake Sturgeon-Weir River Amisk Lake Upper Churchill River Frog Portage Churchill River Trade Lake Keg lake Drinking Lake Nistowiak Lake Mountain Lake Otter Lake Devil Lake Nipew Lake Trout Lake Black Bear Island Lake Sandfly Lake Pinehouse Lake Sandy Lake Dreger Lake Knee Lake Primeau Lake Dipper Lake Shagwenaw Lake Lac Ile-a-la-Crosse Churchill Lake Peter Pond Lake La Loche River Lac la Loche

Arctic Divide Methye Portage Clearwater River Lower Athabasca Athabasca River Lake Athabasca Peace River Peace River Dinosaur Lake Pacific Divide Williston Lake Parsnip River Arctic Creek Arctic Lake Portage Lake Fraser River Pacific Lake James Creek Herrick Creek McGregor River Fraser River Overland - Pacific Alexander Mackenzie Heritage Trail Blackwater/West Road River Bella Coola River Dean Channel Deh Cho Slave River Great Slave Lake Deh Cho (Mackenzie River)