By the evening peak hour flooding and overturned trees and power lines had closed roads across the city including in Darlington, Albion Park and North Narrabeen, Marayla and Glenfield.

Arterial roads in and out of the city and to the western suburbs were reduced to a standstill. Motorists were reporting 10-kilometre commutes taking longer than two hours and a solid line of traffic about 15 kilometres long stretched between Five Dock and Parramatta.

Cars travelling on Pittwater Road in Manly Vale were flooded up to their tyres.

Power was cut to more than 100 sets of traffic lights across the city, Transport Minister Andrew Constance said.

Most of the city's ferry services were cancelled, including between Circular Quay and Manly and the Palm Beach services. The Parramatta River ferry was closed between Parramatta and Rydalmere. Early morning commuters from Manly reported an intensely rough ride in eight-metre swells before the service was cancelled.

Flooding and obstructions caused the partial closure of the Central Coast and Hunter lines. An overturned tree partially closed the north shore line, between Chatswood and Hornsby, the second time travellers on the   line were disrupted by a fallen tree on Tuesday.

By 7 pm those delays had extended to southbound trains on the north shore line. Passengers said trains into the city were running slow to navigate waterlogged tracks around Town Hall station.

Premier Mike Baird urged workers to go home early, about lunchtime, to stagger the usual peak-hour strain on the city's trains.

But passengers reported train services were heavily crowded by about 4 pm.

Buses were delayed and diverted across about 15 Sydney suburbs, many in the city's north. Services in and out of the city and to its west were delayed by at least 30 minutes on Tuesday evening, but travellers on all services were warned to expect delays.

But the city's light rail was listed as running according to normal schedule.

Transport disruptions began early in the day. By the middle of the early  peak hour, at 8am, authorities had already advised commuters across Sydney to cancel all non-essential travel and go home early.

But many had already been delayed for hours.

An overturned tree at Wahroonga delayed trains from the north shore into the city in the middle of peak hour.

Travel by sea was also disrupted and the city's harbour master took the rare step of declaring Sydney closed to ships. The decision was made in response to "cyclonic" conditions and swells in excess 10 metres were recorded in seas around Sydney with winds exceeding 45 knots.

Sydney Harbour, Port Botany and Port Kembla were declared closed from about 8 am on Tuesday, for a period of up to 48 hours. Operations at the Port of Newcastle were also suspended.

That left a cruise ship, the Carnival Spirit, moored outside Sydney Heads. The ship is carrying about 2500 passengers.

"There's a risk of ships 'surfing'," a spokesman for the Port Authority said. "Notwithstanding the fact we're talking about something that's 80,000 tonnes, in these conditions there's a risk you lose control of the vessel.

"It's better off staying where it is for the time being."

No other cruise ships were scheduled to enter the Harbour on Wednesday and Thursday, the spokesman said.