The shipsboats had their torpedo tubes moved to the middle of the hull and angled outboard. This made available the required large space in the bow for the BQQ-2 (BQQ-5 as modernized from the late 1970s) sonar sphere, a new and powerful low-frequency detection sensor. Initially armed with [[Mark 37 torpedo]]es, by the late 1960s they carried the improved [[Mark 48 torpedo|Mark 48]] and the nuclear [[UUM-44 SUBROC]] short-range anti-submarine missile, replacing up to six Mk 48s. The ''Thresher''s were the first class fitted with the Mark 113 fire control system that enabled the use of SUBROC; they were later upgraded with the Mark 117 system. In the late 1970s the [[UGM-84 Harpoon]] [[anti-ship missile]] was introduced; typically four were carried in place of Mk 48s.{{citation_needed|date=August 2019}}
The maximum weapons load was 23 torpedoes/missiles or, theoretically, up to 42 Mk 57, Mk 60, or Mk 67 [[Naval mine|mines]]. Any mix of mines, torpedoes, and missiles could be included.<ref>''War Machines Encyclopedia'', Aerospace Publishing Ltd., Italian version printed by De Agostini, pp. 526–27</ref>