By about 10am, the balloon managed to reach the shore and landed safely.
Large crowds gathered near the shore to watch the dramatic event unfold.
Onlooker Bill Brown, of Cheltenham, said he noticed the balloon flying very low about 8am.
"It was just after 8 o'clock when we saw it coming out over land," he told the Herald Sun.
"It was up really high trying to get the breeze I guess. It as unsuccessful and it just drifted ever so slowly out to sea."
Separately, another hot air balloon ran into trouble this morning, making a surprise landing in a suburban street at Aspendale Gardens.
Resident Cheyne Chalmers told the ABC she woke to a loud burner noise and looked out the window to see the balloon in the street.