In the early days of the Spanish–American War, he was with Admiral William T. Sampson in New York, and arrived off Santiago on June 1, 1898. In order to bottle up the Spanish squadron of Admiral Pascual Cervera y Topete, Hobson took temporary command of the collier "Merrimac", which he would attempt to sink as an obstruction in the channel. The attempt was made early June 3, under heavy Spanish fire, which disabled the steering gear of the collier. Hobson did sink "Merrimac", but was unable to place her in the shallowest part of the channel. With his crew of six, he was picked up by Admiral Cervera himself and treated quite chivalrously.