Police will allege the sexual abuse lasted three years while the man and the girl's mother were living together, however, the assaults allegedly continued after the relationship ended.

The man, who can not be named for legal reasons, fronted Wollongong Local Court on Friday where the disturbing allegations were revealed during his application for release.

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Documents tendered to court said the girl recalled being allegedly touched inappropriately when she would play with her stepfather, however, the alleged abuse escalated into rape in 2016 when the girl's mother was in hospital giving birth.

The man entered the 13-year-old girl's room while she was sleeping and pushed her head into her pillow and allegedly sexually assaulted her.

The girl, who reported the incidents to police this month, alleges her stepfather continued to abuse her consistently for years in nearly identical circumstances in their home south of Wollongong.

After the family moved into a new home away from the stepfather in 2019, police will allege the man stole a key, made a copy and then used it to break in and sexually assault the girl. The girl alleges this occurred twice a month up until the middle of this year.

Police will also allege the man groped his nine-year-old biological daughter multiple times when they went to a local park.

The girls told their mother in October this year after feeling safe as the stepfather no longer came to their home.

The man was arrested on Thursday and in a police interview denied the allegations.

The stepdaughter told police she had trouble sleeping, fearing the man would come into her room to abuse her.

The girls also claim their stepfather could be violent and on occasion would strike or push them.

Police believe the girls' accounts of the alleged abuse are "compelling".

The man was charged with two counts of aggravated sexual assault of a victim under 16 years, two counts of aggravated sexual assault after break and enter, three counts of indecently sexually touching a child under 10 years and three counts of common assault.

He faces up to 20 years in prison on the aggravated sexual assault charges.

In court on Friday, Magistrate Jillian Kiely refused to grant the man bail due to the "very serious allegations" and because he was already on bail at the time of the alleged offences.

The man's case will return to court on December 23.

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