His father was an army officer, General George Mercer Brooke, who died in San Antonio, Texas.

He worked for many years with Commander Matthew Fontaine Maury at the United States Naval Observatory (USNO), charting the stars as well as assisting in taking soundings of the ocean's bottom to determine the shape of the sea floor.

Many believed the sea floor was flat, but all previous soundings as deep as eleven miles (18 km) could not find the ocean bottom.

A sample was sent to Jacob Whitman Bailey at the United States Military Academy, who in November 1853 responded: I was greatly delighted to find that all these deep soundings are filled with microscopic shells; not a particle of sand or gravel exists in them.

[3]The inference in all of this is that the area where the samples came from was the "telegraphic plateau" as called by Maury who had sent out ships to sound those depths at two hundred mile intervals from Newfoundland to Ireland.

Cyrus Field also contacted Samuel Morse regarding the feasibility of transmitting an electric current a distance of 1,600 miles (2,600 km) underwater.

On his return to the United States, he worked with Commodore John Rodgers to prepare the official charts and records of the expedition.

In 1858, he returned to sea on the USS Fenimore Cooper to map the topography of the north Pacific seafloor and to survey the east coast of Japan.

During World War II the Liberty ship SS John M. Brooke was built in Panama City, Florida, and named in his honor.