The expert phase of Coroner Alexander Ho’s inquest into the 3-year-old’s death continued in Invercargill today.
In 2019, Lachie was found 1.2km from his Gore home, face up in an oxidation pond.
Lachie’s father Paul Jones never believed his son drowned and suspected foul play.
Today, Dr Judy Melinek, an expert forensic pathologist, said she had "reasonable medical certainty" that Lachie drowned.
"In my opinion there is sufficient combined investigative and autopsy information to conclude that this death was likely from drowning and not from inflicted injury or some other natural disease process," she said.
An issue raised multiple times throughout the inquest was Lachie’s unmarked feet.
Police say he walked more than a kilometre in bare feet over rough ground, including on sharp gravel.
But Dr Melinek said this did not concern her as there was an explanation for the lack of abrasions.
"Superficial injuries may be obscured by over-hydration of the skin from immersion in water," the witness explained.
"Small children in New Zealand frequently walk around outside barefoot, toughening the soles of their feet over time."
She said that under a microscope, plant material and dirt could be seen in Lachie’s lungs which indicated that he breathed in pond water.
Constable Lachlan MacDonald who pulled the toddler’s body from the water earlier gave evidence there was foam in his mouth.
Dr Melinek said that indicated Lachie breathed in water.
"If you have a person who's killed and then thrown into water . . . they're not going to breathe out water because they're already dead," she said.
The court heard that in some cases, a serious head injury could cause liquid in the lungs and foam in the airways.
The witness explained that while it was possible for a child to have a serious head injury that rendered them unconscious, caused foam in their airways and left no external injury - it was extremely rare.
"If that were the case then I would need evidence," she said.
"We have ample evidence of something that more likely happened."
She agreed that given the circumstances, Lachie’s body should have been sent to Christchurch for a full forensic autopsy, especially because concerns of neglect were raised.
"However, in my opinion, any deficiencies in this autopsy report do not preclude a diagnosis of death by drowning. It is both reasonable and likely that Lachlan Jones drowned based on the autopsy report . . . in totality with the circumstances," she said.
"It would be grasping at straws and speculative to say that because there wasn't an internal examination of the brain conducted . . . that we can not conclude what his cause of death is."
The inquest will continue this afternoon and an investigator being called by Paul Jones’ lawyer is expected to give evidence.
