More rain is expected in the area over the weekend
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Residents living close to the River Thames are being warned to expect more flooding over the next two days.
Peter Quarmby, of the Environment Agency, said: "There's an awful lot of water to come down the Thames."
Hundreds of residents across Berkshire were forced to spend Friday night in emergency accommodation as torrential rain left many towns under water.
Roads in Arborfield, Shinfield, Aldermaston and Pangbourne are closed and trains have been badly affected.
Maidenhead, Thatcham and Newbury were among the places worst hit.
The horses were moved to the stables of rival trainers
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Mr Quarmby, South East Area Manager, added: "The problem now is the Thames is beginning to rise with rain coming down from the Cotswolds - over two months' rain in one day.
"We are expecting to have flooding in Oxford, then that will come down-river and we'll be closely monitoring the Thames through Berkshire and on towards London.
"There could be a serious risk of flooding later on Sunday or Monday."
Hundreds were left without electricity on Friday night and dozens of homes near Brimpton still have no power.
Top horseracing trainer Harry Dunlop had to evacuate his stables in Lambourn as water levels rose.
Twenty horses had to be led away and moved to the stables of other trainers.
Flood warnings remain in place in areas around the rivers Lambourn, Thames, Kennet and Loddon.
The flooding caused chaos in Maidenhead
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More rain is predicted over the weekend and residents are urged to be prepared for possible flooding.
The Royal Borough of Maidenhead and Windsor is advising people not to travel unless it is "absolutely essential".
The council is telling people worried about flooding to "take as many precautions as you can such as blocking outside ground-level air bricks, and creating a barrage of some sort around door thresholds".
West Berkshire Council is opening an advice centre at The Burdwood Centre, Wheelers Green Way, Thatcham.
The Adventure Dolphin Centre, Dolphin House, Whitchurch Road, in Pangbourne is also opening to provide a rest centre for people who were forced to leave their homes.