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March to May and September to November are the best times to visit Australia if you are going to the southern cities. The seasons are reversed, so these are autumn and spring.
The tropical north runs backwards from all of that. Cairns, Darwin and the Great Barrier Reef are wet from November to May and dry from June to October, so the Reef is a winter trip.
Sydney and Melbourne: March to May, September to November
Brisbane and the Gold Coast: April to October, when the summer storms have gone
Perth: September to November, March to May, or December to March for a dry beach summer
Cairns, Darwin and the Reef: June to October
Two northern warnings: box jellyfish are in the water roughly November to May, and cyclones form over the same months. Both are reasons the Reef is best in the middle of the year.
September to November is the best all-round window in the south. Days sit around 20°C, the crowds have not arrived and airfares are below the December peak.
Melbourne is the exception on rain: November is its wettest month. Sydney and Perth are both good now, and Perth's wildflowers are the reason to be in Western Australia in September and October. The Melbourne Cup is in November.
March to May is the other shoulder, and it is warmer in the water. The Christmas crowds have gone, the light is good and the wine regions are at harvest.
Watch two things: Sydney's wettest month is June and the rain starts building through May, and the tropical north is still wet and still has stingers in the water until May. Vivid Sydney runs from late May.
December to February is peak season and the most expensive. It is the Australian school holidays plus Christmas, so beaches, flights and coastal accommodation are all at their fullest.
It is also the wet season in the north and the dry season in Perth. Brisbane and the Gold Coast take their heaviest rain in February; Perth takes almost none from December to February. Bushfire risk peaks now in the southeast, and cyclone risk in the north.
June to August is low season in the south and high season in the north. Sydney runs about 13°C, Melbourne about 10°C, Brisbane and the Gold Coast about 16°C to 17°C and dry.
This is the best time for the Great Barrier Reef, Cairns, Darwin and Uluru. It is also the ski season in the Snowy Mountains and Victorian Alps. Perth is at its wettest, since it has a Mediterranean climate with winter rain.
Cairns is wet from November to May, heaviest December to April, and dry from June to October. Darwin is wet December to March and dry May to September.
So a Great Barrier Reef trip is a winter trip. Wet-season runoff cuts water clarity inshore, though the outer reef is less affected, and cyclones between November and May cancel boat days. June to October gives clear water, calm seas and no stingers.
Box jellyfish are in the water off the northern coasts from roughly November to May, and Darwin's season is October to May. Unprotected beaches close and swimming happens inside stinger nets or in a full suit.
Cyclones form off the north between November and May. A direct hit is uncommon in any one place, but the season is enough to cancel Reef trips and close airports for a day or two. Both risks disappear from June to October, which is the whole argument for going then.