Network Rail Scotland engineers were out in force this morning to assess the impact of heavy rain that battered the country overnight.
Travellers were urged to check with ScotRail before setting off on journeys as many routes were impacted.
Flooding was been identified between Kirkcaldy and Glenrothes, Dyce and Inverurie and at Inverkeilor, between Arbroath and Montrose.
Inverness to Aberdeen services were also suspended due to flooding at several locations along the route.
Network Rail Scotland said: “Our local teams [are] assessing what needs to be done in these areas to reopen the railway.”
Just before 10am, the Edinburgh to Glasgow (via Falkirk) mainline and the Edinburgh to Garrowhill route was however reopened.
Passengers travelling between Dundee and Inverkeithing/Arbroath/Montrose (or within Fife) in either direction were urged to use their tickets on Stagecoach East Bus services.
There were more than 20 flood alerts in place across the UK yesterday.
The Met Office said the last time amber warnings were issued for rain was in March, as forecasters warned of heavy rain across much of the country.
Last night, ScotRail announced its many of its services in regions included in the amber weather warning would end at approximately 7pm.
This morning a spokesperson said: “With Storm Alex bringing heavy rain across parts of Scotland yesterday, and an Amber weather warning being in place, the affected areas need to be checked first thing this morning, to make sure it’s safe to run trains. This means some routes will remain closed this morning, while Network Rail Scotland do this. If you’re due to travel, make sure to check ScotRail.co.uk or @ScotRail on Twitter for the latest live information.”
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