Homicide detectives retraced Stein's steps after he allegedly purchased five 20kg bags of sand from Bunnings, fuelled up his boat and tried to launch it from an inner-Sydney dock.
They also allegedly found a blue tarpaulin in the back of the boat, which was inoperable.
Police allege Stein ended up hiding the heavy barrel containing Charlise's body in dense bushland after struggling to dump it in the Colo River.
The barrel was found late on Tuesday, after a wide-scale investigation was launched last week.
Kallista Mutten is understood to have reported Charlise's disappearance at 8.20am on Friday, January 14, though police were told she was last seen some time on Thursday afternoon.
This sparked a major air and ground search of the bushland surrounding the property.
Yesterday, officers attached to Strike Force Buena conducted a search in the vicinity of the Colo River, about an hour's drive from where Charlise went missing.
The body of a child was located in a barrel. The body is yet to be formally identified but Acting Police Commissioner Karen Webb said the remains were "consistent with the missing 9-year-old".
At about 8.30pm last night, police attended a unit on Riley St, Surry Hills, and arrested Stein, who is engaged to Charlise's mother, Kallista Mutten.
Police released footage of the arrest, after which he was taken to Surry Hills Police Station and charged with murder.
Acting Commissioner Webb said the cause of Charlise's death is yet to be determined and the investigation remains ongoing.
"The search will remain ongoing to look for any clues to help us identify the cause of the death," she said.
"I encourage people to come forward with information. There are still many elements of this investigation that we have to work through to determine exactly what happened from the time the young girl was reported missing up until last night when those remains were found."
Court documents reveal the little girl was killed between 7pm on Tuesday, January 11, and 10am on January 12, but police were not made aware of her disappearance until days later.
Deputy Commissioner Dave Hudson said while investigators are still uncertain of exactly what happened, they were "certain" about a number of facts. He said police will allege Stein placed Charlise's body in the barrel.
"Things will unravel over the next week or so to find a cause of death, the purpose for a death, and try and identify exactly what happened so that the remaining family have some comfort in that," he told reporters.
Stein briefly appeared at Central Local Court on Wednesday from the cells at Surry Hills police station, still wearing the grey Everlast jumper he was arrested in overnight.
His lawyer did not apply for bail but told the court he was suffering longstanding mental health issues and was worried for his safety while in custody on remand.
"Asking for recommendation for a full justice health assessment and he be supplied with his prescribed medication," the lawyer said.
A police prosecutor requested an adjournment of 13 weeks for a brief of evidence due to "the complexities of the matter".
"We require additional time for the order to be served and I ask for an additional four weeks," the prosecutor told the court.
"Eight weeks wouldn't be sufficient for all the evidence to be served in that time."
Magistrate Robert Williams declined the request and adjourned the matter for the scheduled eight weeks.
Deputy Commissioner Hudson revealed police will allege in court that Stein had held phone conversations with the child's mother in the lead up to the body being discovered.
"[There were] a number of telephone conversations with the girl's mother, to purchase a number of sandbags, 20kg sandbags from a hardware store, to fuel a boat and then try and float that boat on the water at one of the docks in inner Sydney," he said.
Police allege they then were able to track his movements, through GPS and CCTV, back to the location where police commenced the search yesterday afternoon.
Kallista Mutten is currently under medical supervision, with Deputy Commissioner Hudson saying she has been "difficult" to approach and contact.
"At some stage, hopefully, when those doctors allow, we will be talking further with her," he said.
He said the investigation is ongoing at, at this stage, there is no evidence to support anything other than that the accused acted alone.
"However, it's still early days in the investigation," he said.
Charlise's biological father, Scott Hensby, spoke out about the horrific situation in a Facebook post earlier on Wednesday.
"Goodbye you beautiful little girl. I love you so much. I miss you every day! You have captured the hearts of the nation and the world, and now those hearts are breaking, with mine," he wrote.
"This doesn't happen! Kids need to be safe. What is wrong with you people????
"We will get the answers for you baby, and we will honour you properly. This is not the end of you or your story."
Police, SES and RFS crews have spent the past five days scouring bushland around the multimillion-dollar Wildenstein wedding venue, where Charlise was staying with her mum and Stein.
The nine-year-old usually lives with her grandmother in Coolangatta, Queensland, but was spending two weeks with her mother during the school holidays.
The murder charges come as questions were raised over missing hours between the time she was reportedly last seen and when police were notified.
Police were told she was last seen sometime on the afternoon of Thursday, January 13, though she wasn't reported missing until the following morning.
While the exact time her family realised she was missing is not yet known, it is possible she was missing for anywhere between 15 to 20 hours before police were notified.
University of Newcastle criminologist, Dr Xanthe Mallett, said it is "quite unusual" for there to be such a long period of time between the child disappearing and it being reported to police.
"I think what is unusual is that she wasn't reported missing for a number of hours. That is quite unusual in a child disappearance," she told Sky News.
"However, we don't know why that was."
Mallett said the first 24 hours after a child disappeared were often critical to the investigation.
On Saturday afternoon, Blue Mountains Police Area Commander acting Superintendent John Nelson said investigators had been working with the family.
"We made a number of inquiries at the scene and commenced a search here in the Mount Wilson area and have been working with the family in terms of their time frame and how we progressed the search from there," he told reporters.
"They've given us a bunch of information."
When asked if the case was being treated as suspicious, Superintendent Nelson said investigators weren't ruling anything out at this stage.
"We are not discounting any scenario at this time because we can't," he said.
"It's a traumatic experience for her family.
"We are here to pull out every stop we can to locate her, and that's why we have all the resources and are continuing (to search)."
The Daily Telegraph reported on Tuesday that investigators have turned their attention to a red ute which had been seen at the property.
Officers seized the vehicle after a man drove it to Penrith police station over the weekend to speak with investigators.
The publication reported police were sifting through hours of CCTV footage from cameras around the area to track the movements of the car.
Neighbours had previously told police they saw a car leaving the Mount Wilson property without headlights on at about 4.30am on Friday.
On Tuesday, a neighbour told the Daily Mail his wife was reading at about 4.30am on Friday last week when she heard the sound of a car moving along the driveway.
"She got out of bed and went to the window and saw a shadow moving," the man claimed.
"It is very quiet here at night and you can see the headlights – there weren't any on."
Investigators also seized a boat over the weekend for "further examination".
Earlier this week there were reports that RFS volunteers discovered multiple sets of footprints on a trail not far from the property where the nine-year-old was last seen.
One print seemed to be "very small and barefooted", Nine News reported.
NSW Police Chief Inspector Gary Sims told reporters "certain items have been found and identified".
"But unfortunately [they] haven't led to anything that gives us a definite indication of her location," he said.
