Bakhuysen started his career as a bookkeeper. He had a very nice handwriting and loved to arithmetic. Working for a wealthy merchant at Amsterdam, he discovered so strong a genius for painting that he relinquished the business and devoted himself to art. He studied first under Allart van Everdingen and then under Hendrik Dubbels, two eminent masters of the time, and soon became celebrated for his sea-pieces.
He was an ardent student of nature, and frequently exposed himself on the sea in an open boat in order to study the effects of storms. His compositions, which are numerous, are nearly all variations of one subject, the sea, and in a style peculiarly his own, marked by intense realism or faithful imitation of nature. In his later years Backhuysen employed his skills in etching and calligraphy.
During his life Backhuysen was visited by Cosimo III de' Medici and Peter the Great. In 1699 he opened a gallery on the topfloor of the famous Amsterdam townhall. After a visit to England he died in Amsterdam on November 17, 1708.