An archaeology team led by an academic from London's Kingston University made the discovery while digging at a Neolithic temple complex at Damerham, located about 24 km from Stonehenge.
Researchers were surprised to find a layer of uncharacteristic orange sand and clay on a site that sits on chalk land.
"The site at Damerham is on chalk land, so we don't often find materials like this that capture and preserve the plant remains - pollen or phytoliths - from a specific time period," said Helen Wickstead from Kingston University.
It was evident that prehistoric people living in the area had also come across the sink hole and excavated the material during their own construction work, Wickstead said.
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A pile of matching waste material was also seen at one of the other mounds.
"We didn't expect to find this and suspect it would have surprised the original architects of the site too," she said.
The prehistoric temple complex at Damerham is unusual because of the number of structures that are focused in one area, Wickstead added.
"The diversity of burial architecture here is intriguing. What is special about this place that meant generation after generation returned to the site to live, hunt, build and commemorate life?" she said.
Wickstead believes the Damerham site holds many more secrets about human life in the Neolithic period.