The new 35-mile line connecting the Capital to Tweedbank in the Borders will pass through Midlothian, joining with the old Waverley Line near Eskbank.
Since its closure in 1969, long sections of the line have been replaced by walking and cycling routes, but these will now be lost.
Midlothian Council has held talks with transport charity Sustrans to ensure all the paths will be replaced.
Among the popular trails being permanently moved is route one of the National Cycle Network in Dalkeith.
The new alternative route between Hardengreen and Thorneybank roundabout will take cyclists via Jewel and Esk College, Ancrum Road, the St David’s housing development, Newbattle Golf Course, Waterfall Park and through Woodburn to link with Salters Road.
Cyclists from Eskbank or Dalkeith travelling to the Capital will have the option of biking to the busy Sheriffhall Roundabout using the shared-use cycleway along the A6106 to Lugton Brae.
Those wishing to avoid Sheriffhall can do so by turning off Lugton Brae to Melville Gate Road leading to Gilmerton Road, crossing the bypass using the flyover bridge.
A Network Rail spokesman said: “As work progresses on the Borders Railway, residents are going to see visible changes in their local area. We understand that the future railway route is currently used by many cyclists and walkers and so we are working with the local council to ensure alternative routes are identified where possible.”
Sustrans said the long-term benefits of the new facilities outweighed the loss of some existing routes.
A spokesman said: “Obviously it is a loss for the current cycle paths to be given over to the new Borders railway, but it is important to take a long-term view.
“The new rail link will provide an alternative, more sustainable form of transport for those who currently commute by car to Edinburgh.”
A Midlothian Council spokesman said: “As a council we’ve already built some of the replacement cycle ways. These routes are not exact replicas of the existing paths. They include shared paths alongside roads, sections through new housing developments and, in some cases, short on-road sections.”