Watkins grew up in upstate New York, but moved to San Francisco with dreams of striking gold. When that venture failed, he worked briefly in delivery and as a bookstore clerk. The bookstore was close to the studio of daguerreotypist Robert Vance, who taught Watkins the basics of photography. With this new skill, Watkins traveled to the Yosemite Valley and made both mammoth-plate images and stereoscopic images. These were some of the first photographs of Yosemite ever seen in the East, eventually capturing the attention of the capitol. President Lincoln signed the Yosemite Grant in 1864, setting aside the land for federal protection.
Watkins continued to shoot in Yosemite for the California Geological Survey, later opening his own gallery just for his award-winning Yosemite images. Though he suffered a series of unfortunate events that led to the loss of his sight and many of his negatives, his images continue to live on.