He was born on June 20, 1731, in Charlestown, Massachusetts, and was one of the "minutemen" who engaged the British at the onset of the American Revolutionary War. Later placed in charge of a small gunboat during the siege of British troops in Boston, Waters was appointed by General George Washington to command the schooner "Lee" on January 20, 1776. He was soon actively engaged in the ensuing assault upon British communications, capturing one enemy vessel in February and another in May. Aided by Warren, Lee seized an armed troopship with 94 Scottish Highlander troops on board in early June. Later in the month, Waters and Lee shared with other vessels the capture of transports "Howe" and "Annabella".