The Aire is very full through the city centre and a flood alert has been issued for the Middle River Aire Catchment through Hunslet and Castleford.
There is also a warning for Meanwood Beck and Wortley Beck, which have began to overflow.
-> LIVE UPDATES: Flooding across Yorkshire blocks train lines and roads and the heavy rain is set to continueThe warnings advise residents to 'be prepared' as flooding is possible.
The flood information service said: "River levels are continuing to rise as a result of persistent rainfall.
"Consequently, flooding of low-lying roads and farmland remains possible.
"Allerton Ings is overtopping at Barnsdale Road near Castleford, and the Washlands are likely to continue spilling into the early hours of tomorrow morning."
Incident response staff are monitoring river levels, which caused heavy flooding on train lines between Leeds and Wakefield Westgate this afternoon.
Northern Rail said that flooded lines have now been reopened, but services between Leeds and Doncaster may still be cancelled or delayed.
The rain is beginning to ease into the evening and there are no further showers forecast in Leeds from 4pm.