A court of inquiry, headed by the local British consul, found the officers of Oneida were responsible for the collision, with Bombay's captain being blamed for not staying at the scene to render assistance – a decision that caused some controversy.

[3] Shortly after commissioning Oneida sailed from New York and joined the West Gulf Blockading Squadron commanded by Flag officer David Farragut.

On 24 April 1862 she participated in the attacks on Forts Jackson and St. Philip below New Orleans, Louisiana, and drove off the Confederate ram which sank the steam gunboat USS Varuna.

In both passages of the Confederate works at Vicksburg, Mississippi – on 28 June 1862 and 15 July 1862 – by the Union fleet under Rear Admiral Farragut, Oneida was second in line.

On 7 August 1862, under the command of Commander George H. Preble, Oneida collided with the steamer Whiteman or Lewis Whitman (sources differ) loaded with dead and wounded troops from the Battle of Baton Rouge, including the body of Brigadier General Thomas Williams, on the Mississippi River near Donaldsonville, Louisiana; the steamer sank with the loss of all hands.

[3][4] Early in September 1862, Oneida failed in an attempt to stop the passage of the Confederate States Navy sloop-of-war CSS Florida into Mobile, Alabama.

The starboard quarter was cut off Oneida and she sank at 6:45 pm in 20 fathoms (37 m) of water with the loss of 125 men, 61 sailors being saved in two Japanese fishing boats.

Inside the wreckage were found many of the bones of the dead sailors, which were interred, at the expense of the salvagers, on the grounds of Ikegami Temple in Tokyo.

In Jinrikisha Days in Japan (1891), Eliza Ruhamah Scidmore tells the story, writing: According to records regarding the Oneida, she was leaving port carrying payment for sales of ammunition and gunpowder to the Japanese government.

The show's salvage team located a shipwreck that matched descriptions of the Oneida, and efforts continue to discover more about the wreckage and remaining contents.