"Squire" Waterton was born at Walton Hall, Wakefield, Yorkshire to Thomas Waterton and Anne Bedingfield.
He was educated at Stonyhurst College in Lancashire where his interest in exploration and wildlife were already evident. On one occasion Waterton was caught by the school's Jesuit Superior scaling the towers at the front of the building; almost at the top, the Superior ordered him to come down the way he had gone up. Waterton records in his autobiography that while he was at the school, "by a mutual understanding, I was considered rat-catcher to the establishment, and also fox-taker, foumart-killer, and cross-bow charger at the time when the young rooks were fledged. ... I followed up my calling with great success. The vermin disappeared by the dozen; the books were moderately well-thumbed; and according to my notion of things, all went on perfectly right.