The Falkirk Wheel boat lift between the Union and Forth & Clyde canals carried canoes for the first time since it was opened in 2012 to mark the opening of the £130,000 route.
It includes 30 dedicated canal access point for canoeists, including at Speirs Wharf, just north of Glasgow city centre, Edinburgh Quay at Fountainbridge, Auchinstarry Marina near Kirkintilloch, and Ratho.
The trail comes a month after the opening of the Pinkston Watersports Centre near Speirs Wharf, which includes a white water course, in a disused basin at the end of the Glasgow branch of the Forth & Clyde Canal.
Scottish Canals said it would take two to four days to complete the trail, with details such as distances and safety advice included in a new guide.
It follows the success of the Great Glen canoe trail on the Caledonian Canal, which has been used by 4,000 canoeists a year since being opened in 2008.
The Edinburgh to Glasgow trail has been developed with Sportscotland, the Central Scotland Green Network, Scottish Natural Heritage and East Dunbartonshire, Glasgow, North Lanarkshire, Falkirk, West Lothian and Edinburgh councils.
The canals were reopened in 2002 in the £78 million Millennium Link project following decades of dereliction and several sections being filled in.
Scottish Canals chairman Andrew Thin said: “We know from the popularity of the newly-opened Pinkston Watersports Centre and the Great Glen canoe trail that paddling is one of the country’s fastest growing sports.
“As this new route runs through some of Scotland’s most socially-excluded areas, it is a great opportunity for canal-side communities to get out on the water and try a new sport right on their doorstep.”
Ron McCraw, of Scottish Natural Heritage, said: “We are sure it will be welcomed by existing canoeists and hope it will attract many new users to enjoy nature, landscapes, healthy activity and new adventures in central Scotland’s great outdoors.”
Mr Matheson said: “Taking to Scotland’s waterways is an excellent way of getting exercise and exploring areas that are off the beaten track.”