Sources say Queensland Rail is treating the issue extremely seriously because until recently train lines at Central Station, Fortitude Valley and Bowen Hills have not previously been cut by heavy rain.

There are suggestions that the 2011 floods may have changed drainage flows, though this is not confirmed, nor substantiated.

Train lines at inner-city train stations were cut on November 19 and 27 in 2014, and the past weekend.

Hundreds of commuters were stranded, with dozens walking home in the rain.

On November 27, a YouTube clip of floodwaters running over train tracks at Brisbane's Fortitude Valley station was viewed more than 17,000 times.

Now an independent inquiry has been launched after last weekend's deluge again covered rail lines and blocked trains at all stations between Roma Street and Bowen Hills.

Queensland Rail executive general manager (Network) Tim Ripper confirmed an investigation was under way to find out why train lines become covered by rainwater.

"We are in the process of engaging an independent engineering consultant to work with Queensland Rail and Brisbane City Council to identify solutions," Mr Ripper said.

Queensland Rail quietly began urgent checks in November 2014 after Brisbane's Central and Fortitude Valley stations were cut by rising floodwaters.

The rising water came from quick run-off from neighbouring properties, Mr Ripper said.

"Despite our best efforts to eliminate flooding issues on the city network, there have been three recent weather events that have caused delays to the city network due to flooding, on 19 and 27 November, 2014, and across the weekend of 21 and 22 March, 2015," he said.

"Flooding was experienced on the rail network between Fortitude Valley and Central stations, due to run-off from surrounding properties."

He said flooding in November 2014 affected all south-east Queensland, not only the rail network.

However, Mr Ripper said the drainage system was working.

"On all occasions, services were suspended in the interest of public safety, and in each case, the water has cleared quickly, due to the robust drainage system in place," he said.

The rising floodwaters blocked trains for 45 minutes between Roma Street and Bowen Hills stations on Saturday and Sunday, he said.

"We understand that our customers have been impacted by flooding on the network," he said.

"We have undertaken significant investigations since the flooding was first experienced in November and are in the process of engaging an independent engineering consultant to work closely with Queensland Rail and the Brisbane City Council to identify solutions."

Queensland Rail had a comprehensive flood mitigation plan in place for the city network, he said.

The plan includes:

- An extensive drainage system across the entire rail system.

- Pumps to quickly drain water away. It  is inspected twice a week as part of a routine maintenance and cleaning program.

Fairfax Media understands the terms of the investigation are being finalised and a "report back" date in now being determined.

"Queensland Rail is committed to addressing this issue and will consult with government on the recommendations," Mr Ripper said.