Dujardin and Hester have been the mainstays of the enormous Olympic success British dressage has enjoyed since 2012 when they won team gold in London, silver in Rio and bronze in Tokyo.
However, two-time individual gold medallist Dujardin -- who in her glory years gave the low key sport the publicity it yearned for -- withdrew last week when a video surfaced of her repeatedly whipping a horse on the legs.
Dujardin got her first job in dressage as a groom at Hester's picturesque stables in Gloucestershire in 2007.
Hester recognised her sublime riding talent and it was with his horse Valegro, who he co-owned and trained, that Dujardin became known as "The Girl on The Dancing Horse", winning individual gold in 2012 and 2016.
Hester, who is riding in his seventh Olympics, said he had not seen 39-year-old Dujardin since the video emerged but he was clearly emotional as he spoke about the incident.
"It is difficult," he said, after he had competed on the opening day of the dressage on the grounds of the Chateau de Versailles.
"I mean, of course it is. I've known her for 17 years. She's a mum, she's got a small child."
"She's paid very heavily for this in a way that you just wouldn't believe," he added.
"I know she will have to accept what the FEI (International Equestrian Federation) gives her, and she will, but I just hope that she's strong enough to be able to come back from that."
'Needs to change'
Hester, who was the youngest ever British rider when he rode in Barcelona in 1992 and is now the oldest in the team in Paris, said the Dujardin in the video was unrecognisable to the one he knew.
"That is not her, that is not the Charlotte I know," he said. "The video was a huge shock to me.
"I had never seen that before."
"It's not obviously on my property.
"Charlotte's made her statement, and she's apologised, and she's given her thoughts on it, which I respect and it's now an ongoing investigation."
Hester said he hoped Dujardin, who has had mental health struggles in the past, would be okay.
He said she was surrounded by people who "want to help her".
"The video was four years ago, people make mistakes and what do we do, never forgive her?" he said his voice quavering.
Hester admitted the video had further damaged the image of equestrian sport, which had question marks placed over its future.
"There is hope that the equestrian can survive, because you just feel there is a huge amount of people that are enjoying it," he said.
"We're having a difficult time, and we have to show the positives of the sport."
He said his yard was open to students from all over the world.
Hester said he agreed with Germany's seven-time Olympic gold medallist Isabel Werth that dressage needs to change.
"We all are making an effort now to show how much we love our horses, how we train them," he said.
"We all know it needs to change."
"But I mean, as we've seen from the sport here the last few days, we've seen amazing sport, we've seen the care everyone's giving, the grooms that work here are incredibly hardworking, how they love and look after the horses."
