In 1761 he was married to Elizabeth Ayers, daughter of William Ayers of Brookfield, Massachusetts, she died within the year and a few months later their infant son was laid to rest beside his mother. In January 1765 he married again, to Persis Rice, daughter of Zebulon Rice of Westborough, Massachusetts, to this union six daughters and two sons were born.
On April 19, 1775 he again enlisted in the army at the onset of the Revolutionary War, he was commissioned a Lieutenant Colonel and charged with the responsibility of building the fortifications about such important towns as Boston and Charlestown, Massachusetts, West Point, New York and Newport, Rhode Island. In 1776 General Washington gave him the assignment to drive the British from Boston. As was typical of Rufus Putnam, he was successful. This success led to many other important assignments, such as Chief Engineer of the army and commander of the 5th Massachusetts regiment. In recognition of his conspicuous service, the Congress in 1782 commissioned him a Brigadier General. Early in 1883 he resigned his commission and returned to his farm and surveying.
General Putnam was probably the outstanding figure in the opening up of the Northwest Territory and was frequently referred to as “The Father of the Northwest Territory”. Under his leadership the Ohio Company of Associates (New England veterans of the Revolution) landed at the mouth of the Muskingum River on April 7, 1788 and founded the settlement of Marietta, the first permanent settlement within the limits of the Northwest Territory.
M. W. B. Putnam was made a Master Mason in American Union Lodge, an army Lodge, in New York in 1779. He was one of ten Brethren who, on June 25, 1790, petitioned for the reorganization of American Union Lodge. At the first meeting held at Campus Martius on June 28, 1790, Rufus Putnam was elected Junior Warden. He later served as Master in 1794, 1798, 1800, the last half of 1801, and in 1804 and 1805.
On January 7, 1808 in Chillicothe on the second day of the meeting called to organize the Grand Lodge of Ohio, Rufus Putnam was elected to the position of Right Worshipful Grand Master, thus becoming the first Grand Master of the Grand Lodge of Ohio. Unfortunately poor health prevented him from discharging the obligations of that office though he lived some sixteen years longer, passing away on May 4, 1824. He was buried in Mound Cemetery at Marietta, Ohio.