The first great influence on the lakes as we know them today was the last Ice Age that dug the footprints of the lakes from north to south and brought about many physical changes. The glacier ploughed and transported away the surface soil and soil producing rock to a depth of several metres. Because of the massive weight of ice that was thousands of metres deep, the land under it was depressed perhaps as much as 30 metres. During the centuries following, the depressed land rebounded upwards, but unevenly, to form the steep ridges between and around the lakes. Thus the land that had been somewhat flat under the ice ended up as valleys with lakes surrounded by rugged hills.
About 11,800 years ago, the area around Bobs and Crow Lakes was free of ice, although the melting front was still only about 90 kilometers further north. An ice cap several thousand metres deep flowed southward over Ontario, most of the rest of Canada and northern USA, reshaping the land and bringing changes which have influenced land use from then onward. It formed a larger version of the present Great Lakes, and an additional inland water body known as the Champlain Sea. The Northwest shore of the Champlain Sea was roughly along the east margins of the Frontenac Axis, from about Pembroke southward to east of Kingston. The East Basin of Bobs Lake was an inlet on the shore of the Champlain Sea and contained salty water. The salty water flowed in from the ocean when the land was sufficiently depressed to permit an inflow, but melting glacial water diluted the salinity.
The Champlain Sea lasted about 2,000 years until most of it drained away when the St. Lawrence River opened to the Atlantic. From then on, water from Bobs Lake flowed out at Bolingbroke as the source of the Tay River.