When Great Britain declared war on Nazi Germany on 3 September 1939, "Nelson" and the bulk of the Home Fleet were unsuccessfully patrolling the waters between Iceland, Norway and Scotland for German blockade runners and then did much the same off the Norwegian coast from 6–10 September. On 25–26 September she helped to cover the salvage and rescue operations of the damaged submarine . A month later, the ship covered an iron ore convoy from Narvik, Norway. On 30 October "Nelson" was unsuccessfully attacked by the near the Orkney Islands and was hit by two of the three torpedoes fired at a range of , none of which exploded. After the sinking of the armed merchant cruiser off the coast of Iceland on 23 November by the German battleships and , "Nelson" and her sister participated in the futile pursuit of them. On 4 December 1939 she detonated a magnetic mine (laid by ) at the entrance to Loch Ewe on the Scottish coast and was under repair in HM Dockyard, Portsmouth until August 1940. The mine blew a hole in the hull forward of 'A' turret which flooded the torpedo compartment and some adjacent compartments. The flooding caused a small list and caused the ship to trim down by the bow. No one was killed, but 74 sailors were wounded.