While the Fort Massapeag site was purchased from Indigenous peoples in 1693, records from the 1680s indicate a nearby Native American village with seven wigwams. However, within roughly three decades, the Indigenous presence in Massapequa diminished, with no Native Americans residing there by the end of the 17th century.
In 1696, Thomas and Freelove Jones became the first permanent European settlers in Massapequa, establishing their residence on land granted by Freelove's father, Thomas Towsend. Interestingly, the land where Fort Massapeag was located remained vacant, serving as a wood source for the Jones family for over two centuries. This area remained undeveloped until the 1930s when the Jones family sold it for housing development.
The 17th-century arrival of Dutch and English settlers marked a significant turning point for the Lenape and Matinecock tribes, who had inhabited Long Island for over a millennium. European colonization led to their gradual displacement due to disease, conflict, and unequal land transactions. By 1700, Indigenous communities were gone from Massapequa, with many moving eastward on Long Island or upstate. Despite these hardships, the Algonquian civilization and the Lenape and Matinecock cultures continue to have lasting impact on Massapequa and Long Island. It is important to remember that many Indigenous people still live on Long Island, and their past cultures remain a critical element in their current lives.