Mackenzie River from the Peace-Athabasca system are significantly slowed by the delta area at the western end of Lake Athabasca causing the lake to rise, and the excess water can only flow out after the rivers have receded. The same phenomenon occurs at Great Slave Lake, which naturally regulates the flow from the Slave River into the Mackenzie. There are river gages at several upstream points along the Mackenzie River. The average flow rate at the outlet of Great Slave Lake is . At Fort Simpson, below the Liard River, it is . At Norman Wells it is , and at the
Mackenzie River and riparian habitat. There are 53 fish species in the basin, none of them endemic. The Mackenzie River has a similar range of fish fauna to the Mississippi River system. It is believed that the two river systems were connected during the Ice Ages by meltwater lakes and channels, allowing fish in the two rivers to interbreed. Fish in the Mackenzie River proper include the northern pike, several minnow species, and lake whitefish. Fish in the southern half of the watershed are genetically isolated from those of the northern half due to large rapids on the Slave River preventing fish