Network Rail maintenance engineers were on site to inspect the line after heavy rain from last night and this morning caused flooding on the tracks.
A train was stuck in floodwaters between Laurencekirk and Craigo, however passengers were safely transferred onto another service.
ScotRail said the flooding affected their Glasgow, Edinburgh and Aberdeen services.
A Network Rail spokesman said: “At roughly 9.30am this morning, a southbound train – Aberdeen to Edinburgh service – got stuck in flood waters between Laurencekirk and Craigo.
"The train wasn’t able to move forward so we got engineers to the site and the passengers were transferred off of that train onto another and the train itself was removed from the location.”
Trains were unable to move between Dundee and Aberdeen and a bus replacement service was implemented.
Passengers were able to get from Edinburgh and Glasgow but could only get a train as far as Dundee.
The line opened shortly before 2pm today, Network Rail announced.