Flood alerts and warnings are in place across Greater Manchester, Lancashire, Merseyside and Cumbria.
Flooding is expected in Highfield Drain and Finchetts Gutter at Abbot’s Mead in Chester, Sefton Street Watercourse at Brierfield in Pendle and Walverden Water in Nelson.
The agency said water levels were rising in those areas due to the recent heavy rainfall.
It said residents were “strongly urged to stay safe and be aware of their surroundings”.
The warning comes after the Met Office issued a amber and yellow weather warnings for parts of the North West on Wednesday, which are due to expire at midday on Thursday.
Forecasters said “flooding and disruption is likely”, as well as “fast flowing or deep floodwater” which could “cause a danger to life”.
Power cuts and loss of other services to some homes and businesses could occur, the Met Office warned.
It is also likely the heavy rain will cause delays or cancellations on trains and bus services, as well as difficult driving conditions and some road closures.
