At the start of the Civil War, 18 July 1936, C-3 was in Cartagena harbour, under command of Teniente de Navío (Lieutenant) Rafael Viniegra González.

They took a patrol line along the Andalusian coast Only two days into the operation, on 20 July, the flotilla entered Málaga harbour, where Guimerá, Viniegra (along with C-3's executive officer), and the rest of the flotilla's senior officers, with the exception of Isaac Peral (C-1)'s skipper, Capitán de Corbeta Lara, were relieved and transferred to the prison ship Monte Toro because they were considered sympathizers of the rebels.

Then she, C-2, and C-6 received instructions to form a patrol arc in front of Ceuta harbour to prevent the entrance of the cruiser Almirante Cervera, which had left Ferrol bound for the Gibraltar Strait.

She repeated the voyage 25 August, in company with C-4 and C-5, where C-3 and C-6 jointly attempted to locate and sink the battleship España and Almirante Cervera, without success.

Despite their proximity, the only survivors were the pilot, García Viñas, and two of C-3's sailors, Isidoro de la Orden Ibáñez and Asensio Lidón Jiménez, who had been topside dumping trash and garbage.

[3] According to the Germans, C-3 was torpedoed by U-34, commanded by Kapitänleutnant Harald Grosse, as part of Operation Ursula;[4] the Republican version differs, claiming that the Spanish boat sank after an internal explosion.

Despite several dives by an ROV (Remote Operated Vehicle) with video camera, it proved impossible to positively identify the wreck, owing to bad visibility.