He was born in Emden, East Frisia, and came to Amsterdam in about 1650, working as a merchant's clerk and a calligrapher. He discovered so strong a genius for painting that he relinquished the business and devoted himself to art from the late 1650s, initially in pen drawings. 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, which often had rough seas.

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 Bakhuizen employed his skills in etching; he also painted a few examples each of several other genres of painting, such as portraits, landscapes and genre paintings.

During his life Bakhuizen was visited by Cosimo III de' Medici, Peter the Great and also worked for various German princes. In 1699 he opened a gallery on the top floor of the famous Amsterdam townhall. After a visit to England he died in Amsterdam on November 17, 1708.