He was educated at Emmanuel College, Cambridge,[1] where he was noted for remarkably intense study.
Watson showed strong Presbyterian views during the civil war, with, however, an attachment to the king, and in 1651 he was imprisoned briefly with some other ministers for his share in Christopher Love's plot to restore King Charles II of England.
Notwithstanding the rigor of the acts against dissenters, Watson continued to exercise his ministry privately as he found opportunity.
Upon the Declaration of Indulgence in 1672 he obtained a licence to preach at the great hall in Crosby House.
After preaching there for several years, his health gave way and he retired to Barnston, Essex, where he died suddenly, while praying in secret.