Wabakimi Provincial Park lies almost entirely in the Arctic watershed just north of the primary (or continental) Atlantic/Arctic Height of Land (see map). Within the park, this drainage system is sub-divided by the secondary Ogoki/Albany Height of Land (see map) which separates the watersheds of the park's two major waterways--the Ogoki and Albany Rivers.

The Ogoki River (see map) bisects the park flowing across it from west to east and most of Wabakimi lies in its drainage basin. All rivers in the southern part of the park drain north into the Ogoki River. From west to east, they are the Flindt, Allanwater, Nemo, Lookout, Boiling Sand, Caribou and Raymond Rivers. From the north, the Palisade River, Webster Creek, Corky Creek, Slim River, Grayson River and Montcrief River flow south into the Ogoki River. The Brightsand River which lies south of Wabakimi is also part of the Ogoki River drainage system. It flows north into the park and becomes the Allanwater River when it passes beneath the Canadian National Railway (CNR) line at Allanwater Bridge.

The Albany River (see map) flows east to Hudson Bay from Lake St. Joseph and abuts the extreme northern boundary of Wabakimi. The Pashkokogan, Misehkow, Greenmantle, Shabuskwia, Witchwood, Attwood and Opichuan Rivers drain north into the Albany River. Due to their respective distances from the nearest road or rail access point and the current lack of reliable canoe route information, the waterways of Wabakimi that lie in the Albany River watershed constitute the least travelled and most remote part of the park.

The only waterway in Wabakimi that lies in the Atlantic watershed is the Pikitigushi River which flows south out of park into Lake Nipigon (see map). Several protected areas also lie in this drainage system including Kopka River, Whitesand, Ottertooth-Obonga and Gull River Provincial Parks as well as Ottertooth and Lake Nipigon Conservation Reserves.

The 'drop and pool' characteristic of these waterways features extended sections of river with barely perceptible currents interspersed with close stretches of roaring, often unrunnable rapids. Occasionally, major rivers widen into very large water bodies the most significant of which are Wabakimi, Whitewater, Whiteclay, Smoothrock, Heathcote, Shabuskwia, Brennan and Smoothrock.

Across the breadth of the park, the elevation difference is less than 100 metres (330'). There are very few waterfalls with significant vertical drops. Many so-called 'falls' are actually 'chutes' where a waterway plunges through a narrow gorge created by a fault in the Canadian Shield or 'cascades' where a waterway drops through a series of smaller waterfalls. Challenging opportunites for whitewater canoeists do exist however, particularly on the Allanwater and Ogoki Rivers and in the adjacent Albany and Kopka River Provincial Parks.

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