The remains of five houses, believed to date to 3,300-3,400 BC, were discovered at Cata Sand on Sanday in 2015 after a storm exposed the stonework on the beach.
But rising sea levels and increasingly bad weather mean that the settlement is likely to disappear again before long.
A team from the University of of the Highlands and Islands Archaeology Institute and the University of Central Lancashire have returned to Cata Sands for a fourth year.
Professor Jane Downes from UHI said: said, “During 2017 and 2018 we excavated a much as we could of the early Neolithic houses, but progress was slow due to the never ending blowing sand, and working between tidal inundations.
"Sea level rises and increased storminess - both relatable to climate change - mean the site will very soon have vanished completely.
"Our aim is to complete the excavation of the house floors and associated pits and hearths before they disappear completely.”
Tests on the floor deposits will hopefully give a full picture as to how these earliest farmers lived inside the houses, Prof Downes said.
The excavations has been funded by public donations, which "flooded in" following an online appeal, she added.
"Sufficient funds to commence the dig and to undertake assessment of the animal and plant remains were raised and the team would like to express their gratitude for the donations from people all over the world." Prof Downes added.
The archaeological site at Cata Sand on Sanday was discovered by four archaeologists – Prof. Jane Downes, Prof. Colin Richards, Chris Gee of the University of the Highlands and Islands, and Prof. Vicki Cummings of the University of Central Lancashire.
They were walking across the sands on their way to inspect a tomb at Tresness at the time.
The archaeologists were led to the site after spotting coarse stone tools along the sands.
A large number of pilot whale bones, which date from the 18th and 19th Century, were found buried in a pit at the site.
The team returned to the site during March 2016 to work at the site and then again in 2017 and 2019, with the series of houses and fragments of stone wall and stone-built hearths discovered.
Prof Downes said: "This was a first for Sanday and although the house remains are incredibly fragile and disappearing fast, floor deposits survive, and bones survives very well – this level of preservation offers a rare opportunity to be able to analyse plant and animal remains and find out how people sustained themselves in this dynamic environment.
"Two tiny and beautifully crafted shell beads were recovered from samples from the 2017 excavation. These give a rare glimpse into the exquisite craft skills that are lacking from other early Neolithic house sites."
Donations can still be made to support the archaeologists working at Cata Sands with money raised now going towards the post-excavation of the site.
To donate, visit www.totalgiving.co.uk