William Flagg was the youngest of three surviving children born to Capt. John and Sarah Flagg. At age thirteen, he shipped as cabin boy aboard the brig Sisters, beginning a long career at sea with Charleston, S.C. as home port. Around 1792, he was given command of his first vessel. In 1794 he was captured, losing his ship; the first of six such losses. In the late 1790's, Flagg enlisted in the United States Navy for two years, becoming a third Lieutenant on the frigate John Adams. Over the next ten years, Capt. Flagg purchased, sailed, sold or lost (by seizure) several vessels. For instance, in 1804, he bought the sloop Delight, sailed to Jacquimel on the south side of Hispaniola for a cargo of coffee. On the return trip, he was intercepted by the French privateer Josephine Bonaparte and interned at Havana.

In 1806 he married Jane Imer in Charleston, South Carolina and between 1811 and 1822, they had seven children. After the Non-Intercourse Act and Trade Embargo, he carried on mostly coastal trading voyages to New Orleans. In 1810, he built the ship Jason in Portsmouth, New Hampshire and went into partnership in shipping with his brother, John (1764-1817). He made two Atlantic crossings in the Jason before laying the ship up during the War of 1812. William Flagg owned a half share of the American privateer Fox whose successful raiding ventures on British shipping earned the captain $236.

He was representative from Dover to the New Hampshire legislature in 1813. In 1815, Flagg sold the Jason and built the Tidewater Farm in Dover. He became an overseer in the spinning room at the Dover Manufacturing Co. and, by 1818, was on the board of directors.

In late 1825, his wife died and on November 30 the following year, he married Harriet (Getchell) Heard of Wells, Maine whose husband, John, had also died the previous year. Between 1829 and 1840, William and Harriet had seven children, three boys and four girls. William died February 12, 1844 at age 73, leaving his residence and estate to his wife. Several of his sons also became sea captains.