Areas including Hackney Wick, Newham and Barking were affected by the downpours, with videos showing cars driving through deep water and people walking nearly knee-deep at times.
Another video showed Pudding Mill Lane DLR station in Stratford underwater after heavy rainfall on Sunday.
Two hospitals reported issues with their emergency departments due to the weather.
Whipps Cross Hospital in Leytonstone said it was experiencing “operational issues due to the heavy rainfall”, while Newham Hospital said its A&E department had flooded in some areas.
A spokesperson for Barts Health NHS Trust said on Sunday evening: “We are experiencing operational issues at Whipps Cross Hospital and Newham Hospital due to the heavy rainfall.
“We are working closely with our local partners to resolve the issues and maintain patient care and – while services remain available for people in an emergency – patients are asked to attend alternative hospitals where they can, to help us put solutions in place as quickly as possible.”
The Met Office issued an amber warning for storms covering London and surrounding counties where homes and businesses are at risk of flooding, which was in place until Sunday evening.
The Environment Agency still has six flood warnings in place across the country’s southeast, while there are 19 alerts for potential flooding active throughout England and Wales.
The torrential downpours came after a heatwave earlier this week brought days of record-breaking temperatures.
Residents in Woodford were forced to use buckets, brooms and wooden boards to create flood defences and scoop the water from their homes.
One local, Mariya Peeva said: “My son went to buy some food from the local shop – by the time he came back the whole street and the pavement were already flooded and the water was coming into our front door.”
Buses were also left stranded on waterlogged roads in Battersea.
Mayor of London Sadiq Khan advised people to “avoid walking or driving through floodwater” and to call 999 in an emergency.
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UK weather: Warnings remain after homes, roads and hospitals in England flooded in deluge of rain