In 1866 Jeffreys retired from the law, and continued a series of dredging operations he started in 1861 aboard the yacht, Osprey, which he later purchased from his brother-in-law.

Accompanied by other specialists in marine life such as Charles William Peach (1800–1886), the Reverend Alfred Merle Norman (1831–1918), George Barlee (1794–1861) and Edward Waller (1803–1873), he dredged the seas around the Shetland Islands, the west of Scotland, the English Channel and the Irish Sea.

[7] In or shortly after 1866 he moved from London to Ware in Hertfordshire, where he bought the Greyfriars Priory, and made it a meeting-place for many British and foreign artists.

He was throughout his life a most indefatigable worker, and at time of his death was still actively engaged upon the description of the deep-sea mollusca dredged by the Lightning and the Porcupine expeditions.

[12] His collection of shells and specimens was bought by William Healey Dall (1845–1927) for the Smithsonian Institution in the United States of America, and was partly donated to the National Museum of Natural History, Washington, D.C. Jeffreys was the author of a number of books and articles on conchology and the mechanics of sea dredging.