Archaeological research at Macktown began with a systematic survey of 30 acres of the 50-acre town platted by Stephen Mack and James Bradstreet in 1836 at the confluence of the Rock and Pecatonica rivers. The initial survey showed that the entire 30 acres contained artifacts from Native American campsites, some dating to as far back as 8,000 years, and historic pioneer households from the Mack era, ending about 1851. Since that survey was completed extensive excavations have been conducted at a shellfish processing area along the Rock River and on the associated Native American campsites on the terraces above; these camps date primarily from the Middle and Late Woodland periods from 2,500 years ago to about 1,200 years ago. Many more Native American camps are yet to be explored.

​The majority of archaeological excavations have been conducted at locations of historic structures that are no longer visible on the
ground surface. These include Hayes Tavern (a mid 19th-century bed and breakfast), the Stephen and Merrill Mack store, the Henry Bates house and shoemaker shop, the William Shores house, and blacksmith shop, and the two still standing Macktown era, the William Whitman House and Store and the Stephen Mack 1839 residence. These excavations have produced the remnants of houses, outbuildings, and thousands of both Native American and pioneer artifacts. Data from these projects provide information about the daily lives of the people who have lived in this resource-rich environment and contribute to the recreation of the area as a living history of mid-19th-century life in Macktown.