Efforts by emergency services to resuscitate Zobbie failed. She was airlifted to the Children's Hospital at Westmead in a critical condition, but was pronounced dead after arrival.
According to the Hornsby Advocate, mum Beccie had gone ashore at the time. It is not known if the toddler was wearing a life jacket.
Beccie and Steve Soetekouw and their children, from Tasmania, had been travelling on their seven-metre yacht, the Sumbawa, for two years.
Beccie documented their adventures on a personal blog and Facebook page, describing their clan as a "large, crazy nomad family".
Family friend Andrea Stebbins told the Seven Network the family had arranged a "buddy system".
"I know the older ones had a lot to do with the younger ones," she said, adding the tragedy was "devastating".
Pictures from the scene showed emergency services working on the little girl on the pier at Brooklyn.
Paramedics who responded to the call described the scene as chaotic and emotional.
Witnesses described seeing the body of a blonde girl wearing a red dress.
"It's a gut-wrenching incident," NSW Ambulance Superintendent Jordan Emery told the Seven Network.
"These paramedics are mothers and fathers themselves, they have siblings, nephews, nieces that same age and we're not immune form that incredible suffering that accompanies jobs like this."
Police have launched an investigation into the incident.