Submarining is, and always has been, a very dangerous profession.  Not only are there other militaries out there looking for submarines, often with hostile intent, but a million things can go wrong at any time.  Sometimes, we know exactly what sank a boat.  Sometimes, they just never came back. Those are referred to as being on "Eternal Patrol.

Charles R. Hinman, Director of Education & Outreach for the USS Bowfin  Submarine Museum & Park in Honolulu has put together an outstanding  site dedicated to to all men lost while serving in the U.S. Submarine  Force:
https://oneternalpatrol.com

Jim Christley has compiled an extensive list of the Lost Boats:

LOST BOATS

Sailing aboard submarines is a hazardous business. They operate in a hostile environment and do constant battle with the sea. On occasion, the sea wins. Sometimes all the crew dies, sometimes there are survivors. Sixty-five submarines built for the United States Navy have been lost during their service -- more than ten percent of the total number of submarines we built. Many were lost during declared wartime when the sea is not the only enemy and sailing in harm's way is a way of life. Others were lost when the sea was the only declared enemy but the hazards of maintaining peace required the submarines be put to sea. This list is for information, so we don't forget -- sailing aboard submarines is a hazardous business.

J. Christley

Sources:
      R: Roberts, Stephen, et al, Registry of US Warships
      D: Dictionary of American Naval Fighting Ships
      Ros: Roscoe, Theodore, Submarine Operations of WWII
      SFLM: Submarine Force Library and Museum Boat Books
      WDR: War Damage Report

JANUARY –
USS S-26 (SS-131) was lost on 24-Jan-1942 with the loss of 46 officers and men when it was sunk after ramming by USS PC-460 in the Gulf of Panama, 14 miles west of San Jose Light.
Sources: R, D, Ros, SFLM, WDR
Remarks: Ship reported dived shortly after sinking. In diveable water off Panamanian coast.

USS Argonaut (SS166) was lost on 10-Jan-1943 with the loss of 105 officers and men when it was sunk off Rabaul near 05° 155N; 153° 50E; (Another location given as 5° 40S; 152° 02 E)
Sources: R, D, Ros, SFLM, WDR
Remarks: Water over 1000'

USS Swordfish (SS-193) was lost on or after 12-Jan-1945 with the loss of 90 officers and men when it was sunk near Yaku Island off Kyushu, water <600' deep near island; ( 27° 00 N; 128° 40 E).
Sources: R, D, Ros, SFLM, WDR
Remarks: Loss declared 15 Feb 45, some use this date.

USS S-36 (SS-141) was lost on 20-Jan-1942 when it was destroyed after grounding on Taka Bakang Reef in Makassar
Strait, Indonesia, Near Makassar City, the crew were all rescued.
Sources: R, D, Ros, SFLM
Remarks: No known reports of wreckage being salvaged or sighted.

FEBRUARY --
USS Shark (SS-174) was lost on 11-Feb-1942 with the loss of 59 officers and men when it was sunk East of Menado,Celebes
Sources: R, D, Ros, SFLM, WDR
Remarks: Loss most likely was the result of one of 3 attacks.11 Feb 42 E off Menado, 17 Feb 42 N off Kendari 21 Feb 42 E of Kendari (Ros).

USS Amberjack (SS-219) was lost on 16-Feb-1943 with the loss of 72 officers and men when it was sunk off Rabaul; Last Contact at 5° 05S; 152° 37E
Sources: R, D, Ros, SFLM

USS Scorpion (SS-278) was lost on 1-Feb-1944 with the loss of 77 officers and men when it was sunk East China Sea.
Sources: R, D, Ros, SFLM, WDR
Remarks: WDR date spread is 1-5-44 to 2-24-44

USS Grayback (SS-208) was lost on 26-Feb-1944 with the loss of 80 officers and men when it was sunk near 25 47N 128-45E.
Sources: R, D, Ros, SFLM, WDR
Remarks: Japanese records indicate 26 Feb, US records state 27 Feb. Dateline difference.

USS Trout (SS-202) was lost on or after 29-Feb-1944 with the loss of 79 officers and men when it was sunk near 22-40N; 131-45 E, middle of Phillipines Basin.
Sources: R, D, Ros, SFLM, WDR

USS Barbel (SS-316) was lost on or after 4-Feb-1945 with the loss of 81 officers and men when it was sunk in southern entrance to Palawan Passage 7° 49.5N; 116° 47.5E Palawan.
Sources: R, D, Ros, SFLM, WDR
Remarks: Loss date could be as late as 6 February, however Japanese records indicate the 4th as the sinking attack date.

MARCH --
USS F-4 [ex-SKATE] (SS23) was lost on 21-Mar-1915 with the loss of 19 officers and men when it foundered off Honolulu Harbor.
Sources: R, D, SFLM
Remarks: Hulk raised and reburied off Serria 13 north of Submarine Base, Pearl Harbor.

USS Grampus (SS-207) was lost on or after 5-Mar-1943 with the loss of 72 officers and men when it was sunk in the Blackett Strait; Possibly in Vella Gulf, last contacts at 4° 55S; 152° 30 E
Sources: R, D, Ros, SFLM, WDR

USS Triton (SS-201) was lost on 15-Mar-1943 with the loss of 74 officers and men when it was sunk at 0° 09N; 144° 55E
Sources: R, D, Ros, SFLM, WDR

USS Kete (SS-369) was lost sometime on or after 20-Mar-1945 with the loss of 87 officers and men when it was sunk somewhere between 29° 38N; 130° 02E and Midway.
Sources: R, D, Ros, SFLM, WDR
Remarks: R states probably sunk offNansei Shoto on or about 20 Mar 45, WDrR gives date spread of 3-20-45 to 3-31-45

USS Trigger (SS-237) was lost on 28-Mar-1945 with the loss of 91 officers and men when it was sunk in area 32° 16N-30° 40N by 132° 05E-127° 50E, (Maybe near 32° 16N; 132° 05E).
Sources: R, D, Ros, SFLM, WDR

USS Perch (SS-176) was scuttled on 3-Mar-1942 30 Miles NW Soerabia, Java (60 officers and men were taken prisoner, 52 survived the war).
Sources: R, D, Ros, SFLM, WDR
Remarks: All crew survived sinking and were rescued by Japanese forces. Reportely the wreck has been located and dived.No written report seen.

USS Tullibee (SS-284) was lost on 26-Mar-1944 with the loss of 79 officers and men when it was sunk in operating area just north of Palau. (One man was taken prisoner and he survived the war)
Sources: R, D, Ros, SFLM, WDR

USS H-1 (SS-28) was lost on 12-Mar-1920 with the loss of 4 officers and men when it Grounded, Magdalena Bay, Mexico, was sunk in 9 Fathoms while being towed off.
Sources: R, D, SFLM
Remarks: Hull reported located in 1995. Return expeditions have not relocated hull. Likely to be buried in sand and uncovered only periodically.

APRIL --
USS Pickerel (SS-177) was lost on 3-Apr-1943 with the loss of 74 officers and men when it was sunk within lume of Shiramuka Light off Honshu. (AKA Shiranuka Light)
Sources: R, D, Ros, SFLM, WDR
Remarks: Ros discusses date discrepancy.

USS Snook (SS-279) was lost sometime after 8-Apr-1945 with the loss of 84 officers and men when it was sunk within 100 miles East of 18° 40N; 111° 39E, near Hainan Island
Sources: R, D, Ros, SFLM, WDR
Remarks: R states missing after 8 April. Ros states could have been later up to late May. WDR gives date spread of 4-8-45 to 4-20-45

USS Thresher (SSN-593) was lost on 10-Apr-1963 with the loss of 129 officers and men when it was sunk while on sea trials near Isle of Shoals.
Sources: Personal
Remarks: On line handling party when boat left Portsmouth. Dived regularly for survey.

USS Grenadier (SS-210) was scuttled 22-Apr-1943 after serious damage by aircraft near Penang, ~ 10 Miles West of Lem Voalan Strait (61 officers and men were taken prisoner, 57 survived the war).
Sources: R, D, Ros, SFLM, WDR
Remarks: No losses in the scuttling operation, all crew rescued by Japanese forces.

USS Gudgeon (SS-211) was lost on 18 April-1944 with the loss of 80 officers and men when it was sunk off Saipan near Maug Island.
Sources: R, D, Ros, SFLM, WDR
Remarks: Loss declared after 14 May 44. Ostlund says his research shows loss northeast ofIwo Jima. On 18 April. WDR date spread 4-7-44 to 5-12-44

MAY --
USS Lagarto (SS-371) was lost on or shortly after 4-May-1945 with the loss of 88 officers and men when it was sunk in off Malay Coast in or near the Gulf of Siam 7° 55N; 102° 00E.
Sources: R, D, Ros, SFLM, WDR
Remarks: Diveable water of less than 200 feet

USS Scorpion (SSN-589) was lost on 27-May-1968 with the loss of 99 officers and men when it was sunk while in transit from Med, West of Azores.
Sources: R, SFLM
Remarks: Regularly divedfor survey HMC Saville from Seadragon was Doc on Scorpion.

USS Squalus (SS-192) was lost on 23-May-1939 with a loss of 26 officers and men when it flooded and sank off Portsmouth, NH.
Sources: R, D,SFLM

USS Stickleback (SS-415) was lost on 30-May-1958 when it sank off Hawaii while being towed, after collision with USS Silverstein (DE-534). All the crew were taken off prior to sinking.
Sources: R, D, SFLM

JUNE --
USS O-9 (SS-70) was lost on 20-Jun-1941 with the loss of 34 officers and men when it foundered off Isle of Shoals, 15 miles from Portsmouth NH, 42° 59' 48"N; 20° 20' 27"W
Sources: R, D, SFLM
Remarks: Depth 400 feet. Reported dived 2001. Visibility nil, side scan sonar images only.

USS R-12 (SS-89) was lost on 12-Jun-1943 with the loss of 42 officers and men when it foundered off Key West, 24° 24' 30"N; 81° 28' 30"W
Sources: R, D, Ros, SFLM, WDR
Remarks: Reportedly dived, no published report seen yet.

USS Herring (SS-233) was lost on 1-Jun-1944 with the loss of 80 officers and men when it was sunk within shore battery range of Point Tagan, Matsuwa Island, in Kurlies.
Sources: R, D, Ros, SFLM, WDR

USS S-28 (SS-133) was lost on 4-Jul-1944 with the loss of 50 officers and men when it foundered off Hawaii , while operating with USCGC Reliance
Sources: R, D, Ros, SFLM, WDR

USS Golet (SS-361) was lost on 14-Jun-1944 with the loss of 82 officers and men when it was sunk near 41° 04N; 14° 13E Sources: R, D, Ros, SFLM, WDR
Remarks: R states NW ofHonshu

USS Bonefish (SS-223) was lost on 18-Jun-1945 with the loss of 86 officers and men when it was sunk in Toyama Wan; Near Suzu Misaki; 37° 18N; 137° 25E;
Sources: R, D, Ros, SFLM, WDR

USS S-27 (SS-132) was lost on 19-Jun-1942when it grounded off Amchitka Island, 400 yds off island Near St Makarius Point (near Constantine Harbor), all the crew were rescued
Sources: R, D, Ros, SFLM
Remarks: Diveable water

JULY --
USS Runner (SS-275) was declared lost 1-Jul-1943 with the loss of 78 officers and men when it was sunk somewhere between Midway and Hokkaido.
Sources: R, D, Ros, SFLM, WDR
Remarks: Location not known, cause not known, date of loss not known. Declared lost date used. WDR gives date spread as 5-28 to 7-4-43

USS Robalo (SS-273) was lost on 26-Jul-1944 with the loss of 84 officers and men when it was sunk 2 miles off west coast of Palawan.
Sources: R, D, Ros, SFLM, WDR
Remarks: Possibly diveable water.

AUGUST --
USS Grunion (SS-216) was lost on 1-Aug-1942 with the loss of 70 officers and men when it was sunk near entrance to Kiska (Alaska) Harbor
Sources: R, D, Ros, SFLM
Remarks: Possibly diveable water. WDR states 7-30-42 to 8-6-42

USS Harder (SS-257) was lost on 24-Aug-1944 with the loss of 80 officers and men when it was sunk off Caiman Point, Luzon, RPI
Sources: R, D, Ros, SFLM, WDR
Remarks: Possibly diveable water.

USS Flier (SS-250) was lost on 13-Aug-1944 with the loss of 80 officers and men when it was sunk in Balabac Strait near Mantangule Island.
Sources: R, D, Ros, SFLM, WDR
Remarks: One secondary source stated 8 men survived and were taken prisoner. Ros and SFLM state correctly that eight men survived and were rescued by USS Redfin on 30 August 1944

USS Bullhead (SS-332) was lost on 6-Aug-1945 with the loss of 84 officers and men when it was sunk in West end of Lombok Strait.
Sources: R, D, Ros, SFLM, WDR

USS S-39 (SS-144) was lost on 14-Aug-1942 when it was destroyed after grounding on reef south of Rossel Island Louisande Archipelago. All the crew were rescued.
Sources: R, D, Ros, SFLM, WDR
Remarks: Hulk reported sighted in 1978

USS Cochino (SS-345) was lost on 26-Aug-1949 when it was sunk in Norwegian Sea after fire, one man from Cochino and 6 men from USS Tusk were lost in the rescue operation.
Sources: R, D, SFLM

SEPTEMBER --
USS Pompano (SS-181) was lost on 1-Sep-1943 with the loss of 76 officers and men when it was sunk off the northeast coast of Honshu
Sources: R, D, Ros, SFLM, WDR
Remarks: WDR gives date spread as 8-20 to 9-27-43

USS Grayling (SS-209) was lost on 9-Sep-1943 with the loss of 76 officers and men when it was sunk in or near Tablas Strait, PI.
Sources: R, D, Ros, SFLM, WDR
Remarks: WDR gives date spread as 9-9 to 9-12-43

USS Cisco (SS-290) was lost on 28-Sep-1943 with the loss of 76 officers and men when it was sunk in Sulu Sea west of Mindinao, 9° 47N; 121°44 E
Sources: R, D, Ros, SFLM, WDR

USS S-51 (SS-162) was lost on 25-Sep-1925 with the loss of 32 officers and men when it was sunk after collision with SS City of Rome off Block Island.
Sources: R, D, SFLM
Remarks: Hull raised, studied and scrapped.

USS S-5 (SS-110) was lost on 1-Sep-1920 when it foundered off Deleware Capes 1Sept20 40 miles offshore. All the crew
escaped through a hole cut in hull in the tiller room.
Sources: R, D, SFLM
Remarks: Hull towed by US Battleship Ohio until it foundered about 5 miles from sinking point. Dived. Metal from hole in Navy Memorial Museum.

OCTOBER --
USS Wahoo (SS-238) was lost on 11-Oct-1943 with the loss of 79 officers and men when it was sunk in or near La Perouse Strait.
Sources: R, D, Ros, SFLM, WDR
Remarks: Rumors of searches but no reports of finding the ship.

USS Dorado (SS-248) was lost on 12-Oct-1943 with the loss of 78 officers and men when it was sunk in Western Atlantic, possibly near Cuba.
Sources: R, D, Ros, SFLM, WDR
Remarks: Ship not found and demise is speculated as either being caused by an unknown U-boat, a patrolling B-24 or by
accident.

USS Escolar (SS-294) was lost on or after 17-Oct-1944 with the loss of 82 officers and men when it was sunk somewhere east of 33° 44N; 127° 33E; heading for 33° 44N; 124° 06E.
Sources: R, D, Ros, SFLM, WDR
Remarks: Declared lost sometime after 13 November 1944, later revised. WDR gives date spread as 10-17-44 to 11-3-44

USS Shark (SS-314) was lost on 24-Oct-1944 with the loss of 90 officers and men when it was sunk in channel midway between Hainan and Bashi Channel; 20° 41N; 118° 27E.
Sources: R, D, Ros, SFLM, WDR
Remarks: R states sinking off Southern Formosa.

USS Seawolf (SS-197) was lost on 3-Oct-1944 with the loss of 102 officers and men when it was sunk just north of Morotai, between PI and Indonesia, by USS Rowell; 02° 32 N; 129° 18E.
Sources: R, D, Ros, SFLM, WDR
Remarks: Sunk by own forces in submarine safety zone.

USS O-5 (SS-66) was lost on 11-Oct-1923 with the loss of 2 officers and men when it was sunk after collision with SS ABABGAREZ (United Fruit) off Panama Canal.
Sources: R, D, Ros, SFLM
Remarks: Hull raised and scrapped.

USS S-44 (SS-155) was lost on 7-Oct-1943 with the loss of 56 officers and men when it was sunk on 5th patrol off Paramushiru, Kuriles (Northern); One day out of Attu (2 men were taken prisoner, both survived the war).
Sources: R, D, Ros, SFLM, WDR

USS Tang (SS-306) was lost on 25-Oct-1944 with the loss of 83 officers and men when it was sunk in north end of Formosa Strait in vicinity of Turnabout Island. (Nine of the crew were taken prisoner and survived the war).
Sources: R, D, Ros, SFLM, WDR
Remarks: In diveable water in PRC territory

USS Darter (SS-227) was lost on 24-Oct-1944 when it became grounded on Bombay Shoal off Palawan then was destroyed. All the crew were rescued by USS Dace.
Sources: R, D, Ros, SFLM, WDR
Remarks: Portions of hull remained as of 1998

NOVEMBER --
USS Corvina (SS-226) was lost on 16-Nov-1943 with the loss of 82 officers and men when it was sunk just south of Truk; (Attack at 151° 10E; 5° 50N)
Sources: R, D, Ros, SFLM, WDR
Remarks: Sunk by IJN submarine. Deep water

USS Growler (SS-215) was lost on 8-Nov-1944 with the loss of 84 officers and men when it was sunk in South China Sea. Sources: R, D, Ros, SFLM, WDR

USS Albacore (SS-218) was lost on 7-Nov-1944 with the loss of 86 officers and men when it was sunk near 41° 49N; 141° 11E in channel between Hokkaido and Honshu.
Sources: R, D, Ros, SFLM, WDR
Remarks: No reports of finding wreckage. Diveable water.

USS Scamp (SS-277) was lost on 16-Nov-1944 with the loss of 83 officers and men when it was sunk off Inubo Saki near Tokyo Bay.
Sources: R, D, Ros, SFLM, WDR
Remarks: R states South of Tokyo Bay. WDR gives date spread as 11-9-44 to 11-16-44

USS Sculpin (SS-191) was lost on 19-Nov-1943 with the loss of 40 officers and men when it was sunk north of Groluk Island near Truk. (42 officers and men were taken prisoner, only 21 survived the war)
Sources: R, D, Ros, SFLM, WDR
Remarks: Scuttled by crew, after severe damage by enemy forces.

DECEMBER --
USS S-4 (SS-109) was lost on 17-Dec-1927 with the loss of 34 officers and men when it was sunk after ramming by USCG Paulding.
Sources: R, D, SFLM
Remarks: All but 4 men died within hours in engineroom and motor room due to asphyxiation. Four men trapped in torpedo room survived for possibly 60 hours.

USS Capelin (SS-289) was lost on or after 1-Dec-1943 with the loss of 76 officers and men when it was sunk off Celebes possibly off Kaoe Bay; Halmahera 1° 34N; 123° 07E or in Molukka Passage.
Sources: R, D, Ros, SFLM, WDR
Remarks: R states after 2 December 43. Ros states an attack was made by IJN on 23 Nov and also a reported sighting by Bonefish of a US sub on 2 December. No reports from boat made after leaving Darwin around 17 November 1943. No declared lost date found. WDR date spread is 11-23 to 12-9-43

USS F-1 [ex-CARP] (SS-20) was lost on 17-Dec-1917 with the loss of 19 officers and men when it was sunk after collision with USS F-3 off San Clemente.
Sources: R, D, SFLM
Remarks: Dived and photographed by DSRV in 1997

USS Sealion (SS-195) was lost on 25-Dec-1941 when it was scuttled in Manila Bay after damage at Cavite
Sources: R, D, Ros, SFLM, WDR
Remarks: Bombed on 10 December 1941 with the loss of 5 officers and men. Damage was sufficient to preclude removal to home waters when Philippines were surrendered. Scuttling took place on 25 December. Portions of wreckage remained in place until late 1950's when it was sold for scrapping.