While steaming north of Hispaniola and Puerto Rico on 14 February 1939, Milwaukee discovered the deepest place in the Atlantic Ocean. The spot—which has a depth of —is now known as the "Milwaukee Deep". By January 1941, the ship had returned to Cruiser Division 2 which was now assigned to the Caribbean Patrol, commanded by Rear Admiral Jonas H. Ingram, part of the Neutrality Patrol established after the war began. Cruiser Division 2 was ordered to patrol the Atlantic between Trinidad, the Cape Verde Islands and the eastern bulge of Brazil in April, although Milwaukee was not immediately available. The ship, escorted by the destroyers and , began her first patrol in May, making a port visit to Recife, Brazil, on 1 June, before returning to San Juan, Puerto Rico. These patrols continued in the same manner for most of the rest of the year. World War II South Atlantic Milwaukee, commanded by Captain Forrest B. Royal, was being overhauled in the Brooklyn Navy Yard when the Japanese attacked Pearl Harbor on 7 December. The ship escorted a convoy to the Caribbean from New York on 31 December and then escorted eight troop transports from the Panama Canal to the Society Islands. She rejoined the South Atlantic Patrol Force upon her return and spend the next two years making patrols between Brazil and the African coast. On 19 May she received an SOS from the Brazilian cargo ship SS Commandante Lyra, which had been torpedoed by the off the coast of Brazil. Milwaukee found the freighter abandoned, burning, and listing to port. She rescued 25 survivors from their lifeboats, including the ship's master. Reinforced by her sister and the destroyer , the fires were brought under control, cargo was jettisoned to lighten the ship, and Commandante Lyra was towed to Fortaleza, Brazil. Shortly after, on the night of 20 May, she was attacked by the Barbarigo, commanded by Enzo Grossi (who mistook her for a "Maryland- or California- type battleship") with two torpedoes, which missed and were not even noticed by the American ships; however, Grossi claimed to have sunk his target, and was promoted to Capitano di Fregata (Commander) and decorated with the Gold Medal of Military Valour and the Iron Cross. Two subsequent commissions in 1949 and 1962 would eventually reverse the promotion and the decorations. Rear Admiral Oliver M. Read assumed command of Cruiser Division 2 in