Archaeological excavations began on approximately 174 sites on the scheme in July 2006, and were completed twelve months later. The excavations were carried out by Aegis Archaeology, Headland Archaeology, TVAS Ireland and UCC.

The work was carried out on behalf of Limerick County Council and was funded by the National Roads Authority.

One of the most important sites was located in Tullahedy, just south of Nenagh. It was discovered that a natural gravel mound had been partially enclosed by a palisade during the Neolithic period (c. 4,000-2,400 BC). The remains of two Neolithic houses were also found, as well as a large quantity of artefacts that included stone arrowheads, pottery and one of the largest assemblages of polished stone axes ever discovered in Ireland. This site is unique in Irish archaeology.

It was during the Neolithic period that farming first developed in Ireland. Stone axes were used to clear land for agriculture and people began to live in rectangular wooden houses. This was a significant departure from the more nomadic hunter-gatherer lifestyle characteristic of the preceding Mesolithic period. Evidence for these first farmers was discovered not only in Tullahedy but also in the townlands of Carrigatogher and Ballywilliam to the southwest, and as far south as Sallymount in Co. Limerick.

Evidence for ancient human activity was found throughout the landscape and included the foundations of circular houses from the Bronze Age (c.2,400-600BC), Bronze Age cremation burials and Bronze Age cooking sites, known as Fulachtaí fia (examples of which were found throughout the scheme).

Annaholty bog also yielded important archaeological finds, such as the Iron Age timber road found near Toreheen Island that has been scientifically dated to 40 AD. The road linked two areas of dry ground within the bog, providing safe passage for the Iron Age inhabitants of North Tipperary. A leather shoe was also discovered, perfectly preserved within the peat and believed to be of 12th century date.

Thirteen large enclosures were also excavated, most of which are likely to be early medieval in date. These would have served as defended settlements in the centuries after the coming of Christianity to Ireland. One such enclosure was excavated in Richhill Co. Limerick. It was a bivallate enclosure i.e. it was enclosed by two banks and ditches and this would normally indicate that it was a high status site.

Another impressive site was excavated in Gortybrigane, situated on high ground to the southeast of Birdhill overlooking the River Shannon. This enclosure was 67m in width and its entrance was flanked by two parallel ditches. Evidence of at least three post-and-stake built structures was recorded within the enclosure as well as three corn-drying kilns and quernstone fragments.