Warragamba Dam, Sydney's main reservoir, will begin spilling on Wednesday night for the first time in two years, leading to minor flooding downstream in the Nepean Hawkesbury Valley, the Bureau of Meteorology said.

The level of Lake Burragorang was about 1.2 metres below the spill level as of early Wednesday afternoon, with the height likely to rise further as flows resulting from the east coast low reached the dam, said Hugh Bruist, a senior bureau hydrologist.

Warragamba Dam during an earlier spill.

About 160 millimetres of rain fell into the Wollondilly River catchment upstream of Warragamba in the 48 hours to 9am on Wednesday, the bureau said.