The Gorge is believed to have been formed as a result of a geological fault in the bedrock. Toward the end of the most recent glacial period (12,000 - 9,000 years ago) the receding ice left a channel that was flooded daily with the tides. As the glaciers melted, the release of the immense weight of ice on southern Vancouver Island caused the land mass to rebound, raising it further above sea level. Between 9,000 and 4,000 years ago, this effect isolated the channel of the Gorge from the influence of tides and transformed it into a series of shallow lakes interspersed with bogs. The global sea level eventually rose with further melting of ice sheets, and overrode the effect of the rebound of the land. At that point, between 4,000 and 2,500 years ago, the Gorge once again became a continually flooded tidal inlet and remains so today.
Chris J. Yorath, 2005. Geology of Southern Vancouver Island. Harbour Publishing, Revised Ed.