The region was once the domain of the Mohegan Chief Uncas. The name Mashamoquet is Indian for 'stream of good fishing' and originally was applied to the entire area. Later, Captain John Sabin built a house here to serve as an outpost and the settlement gradually increased in size. In 1723, parish and township privileges were granted and the town became Pomfret, named after Pontefract in Yorkshire, England.

The present park area is actually a combination of three parks: the original Mashamoquet Brook, Wolf Den and Saptree Run. A large portion of the park was public domain even prior to the State Park and Forest Commission's creation in 1914 due to the foresight of the Daughters of the American Revolution who had purchased the Wolf Den parcel in 1899. The State purchased this section from them in 1924 for the original 1899 price and added it to the first Mashamoquet Brook parcel which had been a gift of former Pomfret resident Sarah Fay. These areas, other purchases, and gifts (notably, in 1957, the 148 acre Hotchkins Wolf Den Farm parcel) have been combined to form the present park, which is over 1000 acres.

The most famous feature is the Wolf Den into which, on a night in 1742, Israel Putnam crept and shot a wolf that for years had preyed upon local sheep and poultry. Israel Putnam was later to gain fame as a Major General in the Continental Army during the Revolutionary War.

Near the Den are the Table Rock and Indian Chair natural stone formations. The Indian Chair is a wide seat-shaped ledge. In the section that is now the entrance to Mashamoquet Brook State Park, there once operated a cider mill, grist mill and wagon shop. The mill dam and pond went out during the flood of 1938. Now only the grist mill is still in existence. It is maintained as a museum by the Pomfret Historical Society. The mill is open on a regular basis and staffed by members of the Historical Society who provide interpretation for all interested visitors.