Bidwell was born in Chautauqua County, New York. The Bidwell family moved to Erie, Pennsylvania in 1829, and then to Ashtabula County, Ohio in 1831.. At age 17, he attended and shortly thereafter became Principal of Kingsville Academy.

In 1841 Bidwell became one of the first emigrants on the California Trail. John Sutter employed Bidwell as his business manager shortly after Bidwell's arrival in California. Shortly after the James W. Marshall's discovery at Sutter's Mill, Bidwell also discovered gold on the Feather River establishing a productive claim at Bidwell Bar in advance of the California Gold Rush. Bidwell obtained the four square league Rancho Los Ulpinos Mexican land grant in 1844, and the two square league Rancho Colus grant on the Sacramento River in 1845; later selling that grant and buying Rancho Arroyo Chico on Chico Creek to establish a ranch and farm.

Bidwell obtained the rank of major while fighting in the Mexican-American War. He served in the California Senate in 1849, supervised the census of California in 1850 and again in 1860. He was a delegate to the 1860 national convention of the Democratic Party. He was appointed brigadier general of the California Militia in 1863. He was a delegate to the national convention of the Republican Party in 1864 and was a Republican member of Congress from 1865-1867.

In 1865, General Bidwell backed a petition from settlers at Red Bluff, California to protect Red Bluff's trail to the Owhyhee Mines of Idaho. The U.S. Army commissioned 7 forts for this purpose, and selected a site near Fandango Pass at the base of the Warner Mountains in the north end of Surprise Valley, and on June 10, 1865 ordered Fort Bidwell to be built there. The fort was built amid escalating fighting with the Snake Indians of eastern Oregon and southern Idaho. It was a base for operations in the Snake War that lasted until 1868 and the later Modoc War. Although traffic dwindled on the Red Bluff route once the Central Pacific Railroad extended into Nevada in 1868, the Army staffed Fort Bidwell to quell various uprisings and disturbances until 1890. A Paiute reservation and small community maintain the name Fort Bidwell.

His wife, Annie Kennedy Bidwell, was the daughter of Joseph C. G. Kennedy, a socially prominent, high ranking Washington official in the United States Bureau of the Census who was active in the Whig party. She was deeply religious, and committed to a number of moral and social causes. Annie was very active in the suffrage and prohibition movements.

The Bidwells were married April 16, 1868 in Washington, D.C. with then President Andrew Johnson and future President Ulysses S. Grant among the guests. Upon arrival in Chico, the Bidwells used their mansion extensively for entertainment of friends. Some of the guests who visited Bidwell Mansion were President Rutherford B. Hayes, General William T. Sherman, Susan B. Anthony, Frances Willard, Governor Leland Stanford, John Muir, Joseph Dalton Hooker and Asa Gray.

In 1875 Bidwell ran for Governor of California on the Anti-Monopoly Party ticket. As a strong advocate of the temperance movement, he presided over the Prohibition Party state convention in 1888 and was the Prohibition candidate for governor in 1880.

In 1892, Bidwell was the Prohibition Party candidate for President of the United States. The Bidwell/Cranfill ticket received 271,058 votes, or 2.3% nationwide. It was the largest total vote and highest percentage of the vote received by any Prohibition Party national ticket.

John Bidwell's autobiography, Echoes of the Past, was published in 1900.