Ayer was originally inhabited by the Nashaway, a Nipmuc people that inhabited the lands along the Nashua River and its tributaries. A small settlement was located along the banks of the Nonacoicus Brook, located in the western part of the town. The name of the Nashaway village, its people and the brook, pronounced by locals as , was also recorded in early English sources as 'Nonajcoyjicus,' 'Nonocoyecos,' 'Nonacoiacus' and 'Nonaicoics.' According to the personal manuscripts of Justice Samuel Sewall, best known for his controversial role in the Salem witch trials, he was told sometime in 1698 by Hanah, wife of "Sachem" Ahaton of the Ponkapoag Massachusett tribe, that the name was actually "Nunnacoquis" (modern Wôpanâak Massachusett dialect "Nunahkuqees" ) and signified 'an Indian earthen pot' although literally refers to a 'small dry earthen pot.' The name was likely a reference to a series of small mounds along the banks of the Nonacoicus Brook.