A direct flight from Chicago O'Hare (ORD) to Ottawa (YOW) typically crosses Lake Michigan shortly after takeoff and may also traverse Lake Huron or the northern tip of Lake Erie, depending on the flight path and weather routing.
Flights usually head northeast from Chicago, crossing the southern basin of Lake Michigan, then passing over Michigan's Lower Peninsula or the Straits of Mackinac into Lake Huron airspace before entering Canadian airspace near Sault Ste. Marie or further south over the Bruce Peninsula. The route then continues overland across Ontario to Ottawa.
On a clear day, passengers on the left side (north-facing) often see the coastline of Lake Michigan, the islands of northern Lake Huron (Manitoulin, Drummond), and the vast forests of the Canadian Shield. The Great Lakes are a dominant geographic feature of this short (~1 hr 45 min) flight.
So while you won't cross all five Great Lakes, Lake Michigan and often Lake Huron are part of the aerial journey between the Windy City and Canada's capital.