A vet successfully sedated Poppy and rescuers worked together to attach a sling to the animal.
A Wellington-based chopper from Garden City Helicopters arrived around midday and airlifted Poppy to a neighbouring paddock.
SPCA Wellington chief executive Steve Glassey said Poppy was safe and well and everyone worked together as a team to ensure everyone's safety.
"We've successfully got the horse out of the river and to safety," said Glassey.
"It was a bit touch and go at first with the water levels and weather but everyone came together and worked to save the animal's life.
"We think Poppy is well, the vet was unable to perform a complete check as she was sedated so we will wake her up and then she can have a check over to make sure everything is okay.
"Great outcome for everyone involved."
SPCA staff worked with emergency response teams from the Massey University vet school and the Palmerston North City Council, the Police and Kapiti Coast District animal control.
The owner was at the scene and had put a cover on the horse, who had some minor cuts.
Kapiti Coast District Council's animal control unit was called around 8.30am and then notified the SPCA.
Police were called when a member of the public became disruptive.
Vicky Hale, a member of the SPCA animal rescue unit explained that the horse had been trapped few days but rising waters meant it had to be rescued.
"The horse is called Poppy. We are unsure as to how it got there," said Hale.
"The cost of the helicopter will be covered by Wellington SPCA and donations are welcome."
The rescue will continue throughout the afternoon.
• To donate please visit wellingtonspca.org.nz
NZH