In the depths of the Pacific Ocean, where the water runs cold dark and cold, temperatures are continuing to fall - and it's all because of a period of significant cooling that began in the 16th century.

Although global ocean surface temperatures are on the rise, it seems the message hasn't gotten through to the waters at the bottom of the Pacific. They're lagging a few centuries behind the rest of the world when it comes to temperature patterns, according to new research.

"Climate varies across all timescales," said Earth and planetary scientist Peter Huybers of the Harvard John A. Paulson School of Engineering and Applied Sciences.

"Some regional warming and cooling patterns, like the Little Ice Age and the Medieval Warm Period, are well known. Our goal was to develop a model of how the interior properties of the ocean respond to changes in surface climate."

The Little Ice Age, as it is known, is a period of several centuries of cooling that took place from around 1550 to 1850 CE, following the Medieval Warm Period.

However, in spite of the name, it wasn't actually an ice age, since it seems to have occurred regionally, rather than globally - although exactly what caused it is still unknown.

But the regions it affected were large and numerous, and obviously included the ocean.

And the Pacific Ocean's circulation takes a very long time. Once the water sinks down, it is isolated from the atmosphere (and its temperature) for an estimated 8 to 14 centuries.

This means those waters on that were on the surface during the Little Ice Age may still be cooling the depths as they descend, following behind warmer waters from the Medieval Warm Period.

"These waters are so old and haven't been near the surface in so long, they still 'remember' what was going on hundreds of years ago when Europe experienced some of its coldest winters in history," said physical oceanographer Jake Gebbie of Woods Hole Oceanographic Institution.

"If the surface ocean was generally cooling for the better part of the last millennium, those parts of the ocean most isolated from modern warming may still be cooling."

The team used data and computer modelling to ascertain the deep circulation of the Pacific since the 1870s.

During the 1990s, the World Ocean Circulation Experiment took a number of readings of the Pacific's temperature up to depths of 2 kilometres (1.24 miles).

And between 1872 and 1876, scientists aboard HMS Challenger repeatedly plunged a thermometer into the world's oceans to take over 5,000 temperature readings, also at depths of around 2 kilometres.

"We screened this historical data for outliers and considered a variety of corrections associated with pressure effects on the thermometer and stretching of the hemp rope used for lowering thermometers," Huybers said.

These screened and corrected data were then compared against the more recent data from the WOCE.

Gebbie and Huybers found, as expected, a warming trend closer to the surface - but at depths of between 1.8 to 2.6 kilometres (1.1 to 1.6 miles), the ocean has cooled.

Not by a great amount - only between 0.02 and 0.08 degrees Celsius - but compared to global warming trends on the surface, it's an intriguing result.

And it has implications on how the planet is warming today - showing that previous surface climate changes could still be having an effect on the current rate of climate change.

That's because previous estimates of how much heat has been absorbed by Earth in the 20th century is based on an ocean in equilibrium at the start of the Industrial Revolution.

But this finding indicates that Earth could have absorbed up to 30 percent less heat than these estimates.

"Part of the heat needed to bring the ocean into equilibrium with an atmosphere having more greenhouse gases was apparently already present in the deep Pacific," Huybers said.

"These findings increase the impetus for understanding the causes of the Medieval Warm Period and Little Ice Age as a way for better understanding modern warming trends."

The research has been published in the journal Science.