Knowles was born into a distinguished naval family, with his father rising to the rank of admiral and receiving a baronetcy for his services.

Edward followed him into the navy, and served with several important officers in operations during the Seven Years' War, which he spent mostly in North American waters.

He supported the sieges of Louisbourg and Quebec and made the acquaintance of the natural philosopher John Robison, who spent some time as his mathematics tutor.

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.

[1][b] Knowle's tutor Robison had initially hoped to be made purser of the ship, but found her small size less congenial than the larger men of war he had served on, and left after seeing some service in the Bay of Biscay and Lisbon.

[1] The imminent declaration of war with Spain necessitated the sending of despatches to the British commands at Belle Isle and Lisbon, and Knowles was entrusted with the task.

[4][6] c. ^ This proved to be a fortuitous decision for Robison, who went on to become a respected natural philosopher and inventor, and a Fellow of the Royal Society of Edinburgh.