Rail users were hit by cancellations and delays on Wednesday as torrential rain struck England, Scotland and Wales.
The Met Office has issued a yellow alert for heavy and persistent rain for north Wales and a large swath of central, eastern and north east England lasting until the end of Wednesday.
A yellow warning of thunderstorms covering London and southern England is also in place until 11pm.
As of 7pm, the Environment Agency had issued 49 flood alerts, advising flooding was possible, and 10 flood warnings, which mean flooding is expected and immediate action is needed.
Transport for Wales warned travellers that rail services were being severely disrupted due to flooding.
The lines between Shrewsbury and Chester, and Crewe and Chester, were closed, with attempts being made to provide road transport.
Rail operator Thameslink said a burst water main flooding the railway between Petts Wood and Orpington in London meant trains were running at a reduced speed on all lines.
In Scotland, an outdoor Rod Stewart concert in Aberdeen was cancelled “due to adverse weather conditions”.
Met Office meteorologist Luke Miall warned that the wet weather would continue to blight parts of the country on Thursday.
He said: “As this system pushes up from the south east through the course of the night it will re-intensify and continue through much of Thursday.”
Mr Miall said parts of south east Scotland could see up to 100mm of rain, with an amber alert in place warning of heavy downpours.
The Scottish Government said that the Multi-Agency Response Team, based at the National Traffic Control Centre in South Queensferry, will be monitoring the situation.
According to the Met Office, the wettest ever June for the UK as a whole was in 2012 when an average of 149mm of rain fell.
Mr Miall said this month’s rainfall so far was “still a long way off” breaking that record.
Mr Miall explained that following a dry summer, winter river levels across the country were low, meaning much of the current flooding was surface water flooding that could potentially retreat quickly.
But by the end of Thursday, flooding would increasingly be the consequence of cumulative rainfall, he added.
There are currently no Met Office weather warnings in place for Friday and the weekend, with conditions forecast to be calmer.
The weather is expected to be dryer, warmer and sunnier, but with the risk of heavy and thundery showers in some places.