The entrance to Broken Bay lies between the northern Box Head and Barrenjoey Head to the south. Barrenjoey Lighthouse was constructed in 1881 to guide ships away from the prominent headland. The bay comprises three arms, being the prominent estuary of the Hawkesbury River in the west, Pittwater to the south, and Brisbane Water to the north. These three arms are flooded rivers (rias) formed at a time when the sea level was much lower than it is at the present day.

The Hawkesbury River flows from the confluence of the Grose and Nepean Rivers at the base of the Blue Mountains.

Pittwater is generally accepted to mark the northernmost extent of the greater Sydney area, the Northern Beaches. Pittwater's calm waters make it a popular sailing area. West Head, west of Barrenjoey Head, marks the divide between Pittwater and the Hawkesbury.

Brisbane Water has the towns of Gosford and Woy Woy on its shores.

Lion Island, named for its profile's resemblance to a Sphinx from some viewpoints, is located at the entrance of Broken Bay. Lion Island Nature Reserve covers the entire island, and is home to a colony of fairy penguins.

James Cook recorded "broken land" seen north of Port Jackson just before sunset on 7 May 1770, and named it Broken Bay. However, there has been some controversy over whether what is now known as 'Broken Bay' was what was sighted by Cook.

The colonists have called this place Broken Bay, but it is not what was so named by Captain Cook

Ray Parkin in his book H. M. Bark Endeavour claims that the modern 'Broken Bay' was passed unremarked at night, and that Cook was in fact referring to the area around Narrabeen Lagoon. Matthew Flinders placed Cook's 'Broken Bay' at 33° 42' South, near to the mouth of Narrabeen Lagoon.

Whatever the case, Governor Phillip was the first to examine the present day Broken Bay in a longboat from the Sirius on 2 March 1788.

On 28 November 2005, documentary film-maker Damien Lay claimed that the wreckage of M-24, a Japanese midget submarine involved in the attack on Sydney Harbour in 1942 and disappeared soon afterward, was buried under sand on the seabed, just east of Lion Island. Lay claimed to have confirmed that copper wiring found at the site was consistent with that used in similar Japanese vessels. A few weeks later, New South Wales Planning Minister Frank Sartor announced that sonar scans conducted by the New South Wales Heritage Office at the location specified had found no trace of the lost submarine.