The body of the woman in her 80s was found inside a South Lismore house on Tuesday afternoon, NSW Police said. Another woman in her 80s was found dead in her Lismore home earlier in the day.

Lismore Mayor Steve Krieg says the flood-ravaged city is bracing for more deaths as Fire and Rescue search homes and businesses “probably with the sole purpose to make more grim discoveries, unfortunately”.

“There’s so many houses to go through. So many people still unaccounted for,” he told ABC TV on Wednesday.

“That is, unfortunately, the main job of the day today and we just really need people to stay away … to let these people do the worst job imaginable.”

There are also grave fears for a man who disappeared in floodwaters in Lismore on Sunday and is yet to be found.

Premier Dominic Perrottet will visit Grafton on Wednesday to speak with volunteers and be briefed about the floods engulfing northern NSW communities.

Ballina Hospital was evacuated on Tuesday night due to rising floodwaters, with 55 general medical and rehabilitation patients, moved to Xavier Catholic College.

Just after midnight an evacuation order was issued for Ballina Island with the SES warning half a metre of flooding is expected, with the CBD expected to be inundated on Wednesday, isolating the community.

The Bureau of Meteorology has issued several flood warnings for the Greater Sydney area, including the Upper Nepean at Menangle, the Hawkesbury River at Richmond and Windsor as well as the Colo River at Upper Colo and the Georges River .

People in low-lying areas around Windsor and Pitt Town, northwest of Sydney, have been warned to be prepared to evacuate.

Transport for NSW Chief Operations Officer Howard Collins is urging people to avoid unnecessary travel or allow plenty of extra travel time.

“Flash flooding and heavy rain are affecting roads, transport infrastructure and waterways across the state,” Mr Collins said.

The slow-moving system arrived in Sydney late on Tuesday and the BoM is warning a deepening low pressure system off the Central Coast is expected to drift southwest towards the coast.

The system is forecast to hit central and southeastern districts during Wednesday and overnight into Thursday, with heavy rainfall over parts of the Hunter and Metropolitan, Illawarra, South Coast and parts of Central Tablelands and Southern Tablelands.

Sydney could see 200mm of rain on Wednesday with the heaviest falls in the afternoon.

The intense rainfall and thunderstorms could also cause life-threatening flash-flooding, while wind gusts could exceed 90km/h in some areas.

Warragamba Dam, west of Sydney, is 99 per cent full and threatening to spill.

While the rain has eased in the Northern Rivers region, the disaster is ongoing with some 35,000 people ordered to evacuate.

Lismore residents are no stranger to floods but the most recent inundation of the town has been far worse than expected.

The Wilsons River at Lismore peaked near 14.4 metres on Monday afternoon after a levee constructed to mitigate flooding was overflowed by rising waters in the early hours of the morning.

Thousands of people have lost everything and are sheltering at evacuation centres.

Seventeen councils in northern NSW have been officially declared disaster zones.