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They flew by helicopter to the northern tip of the Chiatibo glacier, where a climate change expert explained how it was retreating.
It is one of the around 7000 of Pakistan's 7200 glaciers that meteorological officials say show signs of melting, citing data gathered over the last 50 years.
Earlier, the Duke and Duchess of Cambridge stopped at an airport in Chitral and been given a traditional feathered mountain hat, similar to one gifted to William's mother Princess Diana during her visit to the area in 1991. They were also given an album of photos of Diana during her visit.
William highlighted the visit to the glacier and the challenge of climate change, a major theme of their five-day trip, in a speech the previous evening at a reception hosted by the British High Commission at Pakistan's national monument in the capital, Islamabad.
"This could lead to a loss of over a third of these vital glaciers in less than a century, with enormous impacts not only on the availability of water, but on agriculture and hydropower generation," William said in his speech.
The Prince said he hoped Wednesday's visit to Chitral would help the couple better understand the challenges residents were facing first hand. "I hope to learn what more we all can do to help prevent and mitigate this impending global catastrophe."
Catherine and William later observed damage and emergency response drills in a village in Chitral that had been hit by floods due to glaciers melting.
They also visited a settlement of the Kalash people, a small indigenous group living in the Chitral region where they met with young people and wore colourful local scarves and headwear while being treated to song and dance.