A 23-year-old woman has pleaded guilty to murdering her two-year-old son who was found drowned at Hillarys Boat Harbour.

Gemma Gaye Killeen pleaded guilty when she appeared in the Supreme Court this morning.

Her plea came just days before she was due to fight the charge in a trial, starting on Monday.

Killeen, dressed in black, was in tears when she appeared in the dock to enter her plea to murdering Te Reringa Kayden Ashley Wetere, in November 2010.

Defence lawyer Sam Vandongen today told the court that Killeen was not pleading guilty on the basis that she intended to kill her son but was instead admitting killing on a "secondary basis".

Killeen's supporters and family were in the court, sitting in a separate section to that of the child's father, Eddie Wetere, and his family. Both families declined to comment as they left the court.

The toddler's body was found floating in Hillarys Boat Harbour, with police called to the marina after Killeen reported her son missing from a southern carpark.

She claimed at the time that the boy unfastened himself from his stroller when she turned away for a moment but after interviewing Killeen and examining security footage, police charged her with murder.

Her car was captured on CCTV footage in a carpark at the northern end of the harbour about 5.40pm.

A sentencing date was set for April 20, with Killeen today remanded in custody.