To get to the islands you will need some form of water transport. To some islands you can catch a scheduled ferry services, either on either Sydney Ferries or Captain Cook/Matilda Ferries. Some tours are offered to the islands, including water transport, either scheduled or private. You can also catch a water taxi, or impose on a friend with a boat to drop you off. You cannot moor a boat on any of the islands except Cockatoo, where a $10 fee applies.
If you catch a Sydney Ferry, it is part of the ferry network. MyMulti tickets ($20/$10) are valid, and a single trip costs the under-10km rate ($5.20/$2.60), and you only pay for the first child in a family group.
Matilda/Captain Cook ferries, and they don't accept the standard Sydney travel tickets, and only sell return tickets to Circular Quay or Darling Harbour ($17/$15) The do offer bundles with other ferry trips, such as their all day explorer ticket ($42/$26). However, it would be cheaper just to buy a Sydney Ferries daytripper than to add on their explorer pass.
Water taxi fares start around $50 and go upwards to around $200 which usually includes the first few passengers. It depends on your starting point and destination. Water taxis can take you between the islands, or from the shore to the islands at your convenience.
There is a scheduled ferry service operated to Fort Denison by Matilda/Captain Cook every day of the week. You can get a return ferry there with Matilda Cruises for $17/$15, which includes the park entry fees, and admission to the museum there, but not the tour or admission to the tower. The ferries depart from Circular Quay at wharf 6.
If you want to take a tour of the island and visit the tower, you need to purchase a ticket which includes the ferry transport 24 hours in advance from the Sydney Visitors Centre at Cadmans Cottage in The Rocks. The National Parks and Wildlife Service run a half-hour guided tour for $27/$17 and $72 for a 4 person family. That includes the ferry trip to the island. Standby tickets are available for the tours from the cafe on the island for $10, but these are subject to availability.
There is a rather upmarket cafe on the island. There is a morning brunch for $47 adults and $43 children (which includes the tour). Lunch is also available.
Sydney Ferries run scheduled ferry services about every hour from 6am until 9pm. The island is a stop for the Parramatta Ferries or for the Balmain Ferries - just check the indicator board at Circular Quay for the next service, or check the Sydney Ferries timetable if you are coming from anywhere else. There is no admission fee to the island.
There is a new marina on the island, and you can moor a boat for a fee. If you have a kayak, it seems acceptable to paddle up the slipway, if you leave your kayak on dry land. If you decide to kayak, make sure you know where you are going. Don't land on the neighbouring Spectacle Island, which is still a working naval base.
Sydney ferries has regular scheduled ferry services to Garden Island on the Watsons Bay route. Make sure you arrive well within the museum opening hours, or you will end up having a ferry trip to Rose Bay instead. Only naval personnel are allowed to disembark after museum hours. No private ferries, private boats, or water taxis are permitted to land or approach Garden Island.
Garden Island is no longer a physical island, with the gap with the mainland being filled in by dockyards long ago. However there is still no access from the mainland, with the island area still isolated by a navy base with no public access. It is sometimes possible for tour buses to transit through the naval base to Garden Island. This is only on approved tours, that don't stop in the naval base.
There is no admission fee to the island.
Shark Island is served by an hourly Matilda Cruises  ferry on weekends and school holidays only. The price of $17/$15 round trip per adult includes the National Park landing fee.
Situated in Iron Cove, just off Rodd Point. Not served by ferries. Access by water taxi or drop off. Island landing fee of $7. Must be booked and paid for in advance, and the island capacity is limited to 100, and single groups are limited to 50. You cannot moor a boat on the island.
Situated near to Double Bay, and not serviced by scheduled ferries. You will need to reserve a place and pay a fee of approximately $7 per head to the National Parks and Wildlife Service. You also cannot moor a boat here.
Goat Island is the nearest island on the western side of the bridge. Goat Island has been open to the public for significant periods in the past, but it is currently closed for redevelopment, with no announcement made as to reopening. The island has been opened on New Years' Eve for some charitable events in the past.
This is a naval base. It is only accessible by tours. Tours have in the past been offered by the Navy and by the National Maritime Museum, but these are one off arrangements for open days and special events. You can have a view over the island from Cockatoo Island.
This island is a recreation reserve. It is being developed and may one day be open to the public.
See and Do
A popular island on the harbour. You can't miss seeing it, it is right in front of the Opera House.
The island was used as a convict prison during the early days of Sydney's settlement. The island was then known as Pinchgut. In 1857 the entire area became a large fort, built to defend Sydney against Russian attack.
Today the island is managed by National Parks. There is a museum that you can visit just by catching the ferry, or you can take a complete tour of the fort and tower by taking the National Parks tour.
Cockatoo Island was used for convicts in the early days of the colony, but later it was developed for shipbuilding and industry. There is no industry remaining on the island, and the space is now parkland and many of the buildings open to explore.
On the lower level of the island you can see Fiztroy Dock and Sutherland Dock, where ships were repaired. Both cut out of the rock of the island. The factories and slipway are open to visit too. Some of the old factories house artistic displays. There are two long tunnels cut out of the rock that go under the plateau. The are both still open to walk walk through. The dog-leg tunnel has a soundscape of what life on the island was like at various times through the history.
On the upper plateau level there are more industrial buildings, lookouts, and a convicts mess. There is also a grass tennis courts available for hire ($10/hour).
Allow at least two hours just to complete the self-guided walks on the island. Longer if you want to stop to see the views along the way.
From the high level on Cockatoo Island you can see across to Spectacle Island and Snapper Island. The slipway faces Spectacle Island, and scenery over there looks very similar to Cockatoo. The island was a naval explosives manufacturing and storage depot for the Australian Navy, and the island is still use by the navy (public landings are not allowed - but there are occasional tours run by the navy for special events). Snapper Island is the smaller island to the left of Spectacle. It was complete reshaped and redesigned to resemble a ship, and was then used for navy training. It is a public reserve now, but is not open to the public.
Garden island was the navy headquarters, shipyards and dock for much of its history. It is no longer an island, with the area between the mainland and the island being filled with dry-docks, ship building and other boat and navy facilities. However the only access is still by ferry, since the remaining naval base is on the strip of land between the mainland and the island.
Much of the naval buildings still remain. Many historic buildings and installations, but many that were still in use up until 10 or so years ago. There is a museum on site, with two levels and extensive displays of the naval history of Sydney and the site. There is a real periscope that is a favourite with the kids. All this with free admission.
There are walks along the waters edge, and steeper tracks with steps going further through nicely kept gardens. There are picnic tables and grassy spots for picnic blankets near the waters edge.
The museum can get a bit crazy when school excursions visit, but you would have to be unlucky to be there with a crowd. Usually the island and museum are very quiet.
You can see the bow of the HMAS Parammatta, and several other memorials and monuments scattered around by the waters edge.
Fort Denison has a nice cafe, under a white marquee with a view facing away from the Opera House to the northern side of the Harbour. It serves brunch as part of the tour. It is open for lunch, and serves modern Australian cuisine, of the big plate small fancy serves style. Mains around around $25. The location, however, is unique. There s is a kids menu, which is quite necessary, given the nature of the food and presentation.
There is a kiosk called the Muster Station Cafe open from 8:30am until 4pm everyday. It sells sandwiches, wraps, quiche, muffins, coffee, beer, wine and soft drinks. There are vending machines on the island too.
There are coin operated barbecues on the island that take $1 coins. You have to bring your own food to barbecue.
There is a cafe in the museum on Garden Island, that servers lunch and coffee for around $10. The food is down-to-earth, fancy burgers and sandwiches style. Still, the value in eating at this harbourside location inside the historic buildings on the Island is unmatchable.
On the other open islands there are picnic tables and grass. Bring a picnic basket and blanket.
Occasionally, they have a concerts or other events, particularly on Cockatoo Island. Generally, however, there is no nightlife or bars on any of the islands, and nighttime access is limited.
There are licenced cafes serving alcohol during the day at both Cockatoo and Fort Denison. You cannot bring alcohol onto either of the islands.
You can stay on on Cockatoo Island, right in the middle of Sydney Harbour, right on the water, and about 10 minutes by ferry from the city centre. Don't count on a late night out, as the last ferry takes you back to the island at 9pm, but you can certainly get an early start if you like. Sites are $45. For $75 you get a site, a tent, mattresses, chairs, and lantern. The pre-erected tents you can hire are closer to the water than the sites where you can pitch our own. The tents comfortably fit two adults, and you can squeeze in a couple of kids too if you are keen, for no extra. They hire sleeping bags on the island, so this accommodation is a possibility even if you didn't bring your camping equipment. There are free hot showers. Lockers are available at $8 per 24 hours.
There are also several houses available to rent on the plateau level,
Staying here around New Years Eve requires booking in August, paying more, and sometimes winning a ballot.
You cannot stay overnight at any other islands.
Mobile reception is comprehensive on all the harbour islands.
You get a good view of Cockatoo Island from the Parramatta Rivercat, or the Woolwich Ferry. Both trips leave from Circular Quay in the City Centre.
If you find Garden Island interesting, there is a very similar experience at the old naval site at Chowder Bay at Middle Head,with the old naval installations open to visitors with amazing views, gardens, history and a harbourside location.
If you find Rodd Island hard to access, you can see all there is to see of this small island on the Bay Run around Iron Cove. Walk, cycle or jog around the 7km path next to the water in Sydney's Inner West.
If you want to see Clark Island, you can get another great view from McKell park. A small park with gardens, and view back to the Harbour Bridge, in Sydney's Eastern Suburbs.
You can get a great shot of the Opera House and Fort Denison while walking across the Harbour Bridge, in The Rocks.
There used to be three other islands in the harbour, Glebe Island, Berry Island, and Darling Island. All of these now form part of the mainland. Glebe Island is a port facility, now largely decommissioned. You can see it from the Anzac Bridge, but it really would only be of interest to historians, or fans of abandoned ports, and access to the area is limited. Berry Island is on the Lower North Shore, and there is a 20 minute interpretive bushwalk there. Darling Island forms an seamless part of the mainland at Pyrmont Bay, in the City West. See those article for details.