There are minimal dangers on Sydney Harbour. It is a naturally deep water port.
There is one reef towards the Sydney Heads called ‘Sow & Pigs’ but it is well marked with four cardinal marks. Simply steer well clear.
As for depth, the Harbour is a flooded valley with quite steep sides giving good clearance.
You need to keep a look out for ferries, they have priority. The circular Quay area is always busy, you need to pass it.