Large sections were destroyed in a Great Flood of 1862,[2] and settlers used stones from the old aqueduct to build homes.

[3] The only significant section that remains is located at the mouth of Canyada canyon on land that was formerly known as Rancho Cañada Larga o Verde owned by the Canet family from 1873 until at least the 1960s.

The Ventura County Cultural Heritage Board sought to prevent further demolition, and the owner built his home over the aqueduct, preserving a 20-foot-long section in his basement.

[8] In recent years, preservationists have raised concerns about the failure of the county to take action to protect the remaining section of the aqueduct on Canada Larga Road.

In 1998, the Los Angeles Times wrote that "the lone surviving significant chunk of what was once the seven-mile San Buenaventura Mission Aqueduct sits forlornly in a weed-filled corner of an orchard near a freeway offramp north of the city.