Adelaide rail commuters are set to endure more months of frustration and delays because of works affecting three city train lines.

The State Government said the Outer Harbor and Grange lines, and about a third of the Gawler line, will be out of action for up to 10 weeks because of the Torrens Rail Junction project.

From September 24 until December 3, Outer Harbor and Grange passengers will be forced to use substitute buses.

On the Gawler line, substitute buses will operate between the city and Mawson Lakes from October 1 until October 16.

The closures are to allow for the removal of three level crossings in Bowden — on Park Terrace, and on Gibson and East streets.

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The State Government said the closures would also allow for excavation to begin on the new rail underpass and an upgrade to Croydon railway station.

"While it is disappointing that we need to disrupt train services to do these works, when they are complete they will have a big impact in reducing delays for both road traffic and rail services," Transport Minister Stephen Mullighan said in a statement.

The work is part of a $238 million upgrade to separate freight and passenger rail lines, and will see the freight line lowered beneath the Outer Harbor line in Adelaide's parklands.

"Once these works are complete, Outer Harbor and Grange trains will no longer need to slow down at these level crossings and the requirement for trains to give way to one another will also be removed, improving the travel times for all services," Mr Mullighan said.

Adelaide's suburban train lines have been closed for extended periods in recent years to allow for upgrades including electrification and track works, and because of problems such as electrical faults.