Edward Knowles was born in 1744, the only son from the marriage of Captain Charles Knowles and Mary Alleyne, the sister of John Alleyne. His father became a noted naval officer, rising to the rank of admiral and receiving a baronetcy for his services to his country. Edward attended Eton College and then followed his father into the navy. He first served with a colleague of his father, Captain Richard Howe, of . He afterwards went out with Admiral Sir Charles Saunders to the Siege of Louisbourg in February 1759, aboard the 90-gun . Accompanying him as his personal mathematics tutor was John Robison, who spent the next few years with Edward, and would later serve with his father as a personal secretary. At Louisbourg Knowles took part in the assault on the 64-gun French ship "Prudent", anchored in the harbour, and was later promoted to lieutenant during the voyage and operations to capture Quebec. He transferred to the 100-gun HMS "Royal William" to serve his commission.