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HELENA's first assignment was with the North Atlantic Fleet, cruising primarily in home waters. During the Spanish-American War, she stood by in Cuban waters, where she saw action several times. On 2 and 3 July 1898, she exchanged fire with the enemy batteries at Fort Tunas, and on 18 July 1898, she was one of the squadron which closed the port of Manzanillo by sinking or destroying eight small vessels there during a vigorous attack.
Ordered to attack Tunas July 2 as a diversion for landings to the East, Helena moved with to within 1,500 yards of the town and at 7:30 a.m. opened fire. The Spanish battery was silenced after thirty minutes and although a charge of shrapnel exploded under the starboard 4-inch gun, there were no American casualties. A number of Spanish soldiers were killed and wounded and one gun destroyed. A second bombardment was ordered late in the afternoon and the troops safely put ashore up the coast.
The following morning Swinburne again moved Helena inshore and was notified that considerable reinforcements had been received overnight. He estimated that over 4,000 troops were now in Tunas, but his mission accomplished, he retired after a brief exchange of fire, returning to Cienfuegos the next day.
Helena joined the ships blockading Manzanillo on July 17, and on the 18th participated in a major attack on shipping in the harbour. At 7:50 a.m. Helena with Wilmington, Hist, Hornet, Scorpion, Osceola and Wompatuck entered the harbour and opened fire on the Spanish defense position. Sustained and accurate fire drove the gunboats Estrella, Delaqado Perrato and Cuba Espanoca from the fight and Guantanamo and Guardian were forced onto the beach. Three transports were set afire and left in flames as the squadron departed. Helena also participated in a second bombardment at Manzanillo on July 26.