At the close of his indentures in 1720, Baker went on a visit to John Forster, a relative, who had a deaf-mute daughter, then eight years old.

[1] His work as therapist caught the attention of Daniel Defoe, whose youngest daughter Sophia he married on 30 April 1729.

In 1744, he received the Copley gold medal for microscopical observations on the crystallization of saline particles.

Under the name of Henry Stonecastle, Baker was associated with Daniel Defoe in starting the Universal Spectator and Weekly Journal in 1728.

Among his publications were A Short History of Speech (1723), The Microscope made Easy (1743), Employment for the Microscope (1753),[5] where he noted down the presence of dinoflagellates for the first time as "Animalcules which cause the Sparkling Light in Sea Water", and several volumes of verse, original and translated, including The Universe, a Poem intended to restrain the Pride of Man (1727).