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From 20 to 30 November 1980, Thomas Washington was on site at the western basin of the Challenger Deep, as part of Rama Expedition Leg 7, again with chief-scientist Dr. A.A. Yayanos. Yayanos directed Thomas Washington in arguably the most extensive and wide-ranging of all single-beam bathymetric examinations of the Challenger Deep ever undertaken, with dozens of transits of the western basin, and ranging far into the backarc of the Challenger Deep (northward), with significant excursions into the Pacific Plate (southward) and along the trench axis to the east. They hauled eight dredges in the western basin to depths ranging from 10,015 metres (32,858 ft) to 10,900 metres (35,800 ft); and between hauls, cast thirteen free vertical traps. The dredging and traps were for biological investigation of the bottom. In the first successful retrieval of a live animal from the Challenger Deep, on 21 November 1980 in the western basin at 11°18.7′N 142°11.6′E, Yayanos recovered a live amphipod from about 10,900 meters depth with a pressurized trap. Once again, other than a brief look into the eastern basin, all bathymetric and biological investigations were into the western basin.

Pacific plate subduction at the Challenger Deep

1976–1977 – RV Kana Keoki – On Leg 3 of the Hawaii Institute of Geophysics' (HIG) expedition 76010303, the 156-foot research vessel Kana Keoki departed Guam primarily for a seismic investigation of the Challenger Deep area, under chief scientist Donald M. Hussong. The ship was equipped with air guns (for seismic reflection soundings deep into the Earth's mantle), magnetometer, gravimeter, 3.5-kHz and 12-kHz sonar transducers, and precision depth recorders. They ran the Deep from east to west, collecting single beam bathymetry, magnetic and gravity measurements, and employed the air guns along the trench axis, and well into the backarc and forearc, from 13–15 March 1976. Thence they proceeded south to the Ontong Java Plateau. All three deep basins of the Challenger Deep were covered, but Kana Keoki recorded a maximum depth of 7,800 m (25,591 ft). Seismic information developed from this survey was instrumental in gaining an understanding of the subduction of the Pacific Plate under the Philippine Sea Plate. In 1977, Kana Keoki returned to the Challenger Deep area for wider coverage of the forearc and backarc.

1984 – SV Takuyo – The Hydrographic Department, Maritime Safety Agency, Japan (JHOD) deployed the newly commissioned 2,600-ton survey vessel Takuyo (HL 02) to the Challenger Deep 17–19 February 1984. Takuyo was the first Japanese ship to be equipped with the new narrowbeam SeaBeam multi-beam sonar echosounder, and was the first survey ship with multi-beam capability to survey the Challenger Deep. The system was so new that JHOD had to develop their own software for drawing bathymetric charts based on the SeaBeam digital data. In just three days, they tracked 500 miles of sounding lines, and covered about 140 km² of the Challenger Deep with multibeam ensonification. Under chief scientist Hideo Nishida, they used CTD temperature and salinity data from the top 4,500 metres (14,764 ft) of the water column to correct depth measurements, and later conferred with Scripps Institution of Oceanography (including Fisher), and other GEBCO experts to confirm their depth correction methodology. They employed a combination of NAVSAT, LORAN-C and OMEGA systems for geodetic positioning with accuracy better than 400 metres (1,300 ft). The deepest location recorded was 10,920 metres (35,830 ft) ±10 m (33 ft) at 11°22.4′N 142°35.5′E; for the first time documenting the eastern basin as the deepest of the three en echelon pools. In 1993, GEBCO recognized the 10,920 metres (35,830 ft) ±10 m (33 ft) report as the deepest depth of the world’s oceans. Technological advances such as improved multi-beam sonar would be the driving force in uncovering the mysteries of the Challenger Deep into the future.

1986 – RV Thomas Washington – The Scripps research vessel Thomas Washington's returned to the Challenger Deep in 1986 during the Papatua Expedition, Leg 8, mounting one of the first commercial multi-beam echosounders capable of reaching into the deepest trenches, i.e. the 16-beam Seabeam "Classic". This allowed chief scientist Yayanos an opportunity to transit the Challenger Deep with the most modern depth-sounding equipment available. During the pre-midnight hours of 21 April 1986, the multibeam echosounder produced a map of the Challenger Deep bottom with a swath of about 5–7 miles wide. The maximum depth recorded was 10,804 metres (35,446 ft) (location of depth is not available). Yayanos noted: "The lasting impression from this cruise comes from the thoughts of the revolutionary things that Seabeam data can do for deep biology."

1988 – RV Moana Wave – On 22 August 1988, the U.S. Navy-owned 1,000-ton research vessel Moana Wave (AGOR-22), operated by the Hawaii Institute of Geophysics (HIG), University of Hawaii, under the direction of chief scientist Robert C. Thunell from the University of South Carolina, transited northwesterly across the central basin of the Challenger Deep, conducting a single-beam bathymetry track by their 3.5 kHz narrow (30-degs) beam echosounder with a Precision Depth Recorder. In addition to sonar bathymetry, they took 44 gravity cores and 21 box cores of bottom sediments. The deepest echosoundings recorded were 10,656 metres (34,961 ft) to 10,916 metres (35,814 ft), with the greatest depth at 11°22′N 142°25′E in the central basin. This was the first indication that all three basins contained depths in excess of 10,900 metres (35,800 ft).

The RV Hakuhō Maru

1992 – RV Hakuhō Maru – The 3,987-ton Japanese research vessel Hakuhō Maru, an Ocean Research Institute – University of Tokyo sponsored ship, on cruise KH-92-5 cast three Sea-Bird SBE-9 ultra-deep CTD (conductivity-temperature-depth) profilers in a transverse line across the Challenger Deep on 1 December 1992. The center CTD was located at 11°22.78′N 142°34.95′E, in the eastern basin, at 10,989 metres (36,053 ft) by the SeaBeam depth recorder and 10,884 metres (35,709 ft) by the CTD. The other two CTDs were cast 19.9 km to the north and 16.1 km to the south. Hakuhō Maru was equipped with a narrow beam SeaBeam 500 multi-beam echosounder for depth determination, and had an Auto-Nav system with inputs from NAVSAT/NNSS, GPS, Doppler Log, EM log and track display, with a geodetic positioning accuracy approaching 100 metres (330 ft). When conducting CTD operations in the Challenger deep, they used the SeaBeam as a single beam depth recorder. At 11°22.6′N 142°35.0′E the corrected depth was 10,989 metres (36,053 ft), and at 11°22.0′N 142°34.0′E the depth was 10,927 metres (35,850 ft); both in the eastern basin. This may demonstrate that the basins might not be flat sedimentary pools but rather undulate with a difference of 50 metres (160 ft) or more. Taira revealed, "We considered that a trough deeper that Vitiaz's record by 5 metres (16 ft) was detected. There is a possibly that a depth exceeding 11,000 metres (36,089 ft) with a horizontal scale less that the beam width of measurements exists in the Challenger Deep. Since each SeaBeam 2.7-degree beam width sonar ping expands to cover a circular area about 500 metres (1,640 ft) in diameter at 11,000 metres (36,089 ft) depth, dips in the bottom that are less than that size would be difficult to detect from a sonar-emitting platform seven miles above.

RV Yokosuka was used as the support ship for ROV Kaikō

1996 – RV Yokosuka – For most of 1995 and into 1996, the Japan Agency for Marine-Earth Science and Technology (JAMSTEC) employed the 4,439-ton Research Vessel Yokosuka to conduct the testing and workup of the 11,000 meter remotely-operated vehicle (ROV) Kaikō, and the 6,500 meter ROV Shinkai. It was not until February 1996, during Yokosuka's cruise Y96-06, that Kaikō was ready for its first full depth dives. On this cruise, JAMSTEC established an area of the Challenger Deep (11°10’N to 11°30' N, by 141°50' E to 143°00' E – which later was recognized as containing three separate pools/basins en echelon, each with depths in excess of 10,900 m (35,761 ft)) toward which JAMSTEC expeditions would concentrate their investigations for the next two decades. The Yokosuka employed a 151-beam SeaBeam 2112 12-kHz multibeam echosounder, allowing search swaths 12–15 km in width at 11,000 metres (36,089 ft) depth. The depth accuracy of Yokosuka's Seabeam was about 0.1% of water depth (i.e. ± 110 metres (361 ft) for 11,000 metres (36,089 ft) depth). The ship’s dual GPS systems attained geodetic positioning within double digit meter (100 metres (328 ft) or better) accuracy.

1998, 1999 and 2002 – RV Kairei – Cruise KR98-01 sent JAMSTEC's two-year-old the 4,517-ton Deep Sea Research Vessel RV Kairei south for a quick but thorough depth survey of the Challenger Deep, 11–13 January 1998, under chief scientist Kantaro Fujioka. Tracking largely along the trench axis of 070–250° they made five 80-km bathymetric survey tracks, spaced about 15-km apart, overlapping their SeaBeam 2112-004 (which now allowed sub-bottom profiling penetrating as much as 75 m below the bottom) while gaining gravity and magnetic data covering the entire Challenger Deep: western, central, and eastern basins.

The Deep Sea Research Vessel RV Kairei was also used as the support ship for the ROV Kaikō

Kairei returned in May 1998, cruise KR98-05, with ROV Kaikō, under the direction of chief scientist Jun Hashimoto with both geophysical and biological goals. Their bathymetric survey from 14–26 May was the most intensive and thorough depth and seismic survey of the Challenger Deep performed to date. Each evening, Kaikō deployed for about four hours of bottom time for biological-related sampling, plus about seven hours of vertical transit time. When Kaikō was onboard for servicing, Kairei conducted bathymetric surveys and observations. Kairei gridded a survey area about 130 km N–S by 110 km E–W. Kaikō made six dives (#71–75) all to the same location, (11°20.8' N, 142°12.35' E), near the 10,900 metres (35,800 ft) bottom contour line in the western basin.

The regional bathymetric map made from the data obtained in 1998 shows that the greatest depths in the eastern, central, and western depressions are 10,922 m (35,833 ft) ±74 m (243 ft), 10,898 m (35,755 ft) ±62 m (203 ft), and 10,908 m (35,787 ft) ±36 m (118 ft), respectively, making the eastern depression the deepest of the three.

In 1999, Kairei revisited the Challenger Deep during cruise KR99-06. The results of the 1998–1999 surveys include the first recognition that the Challenger Deep consists of three "right-stepping en echelon individual basins bounded by the 10,500 metres (34,400 ft) depth contour line. The size of [each of] the deeps are almost identical, 14–20 km long, 4 km wide." They concluded with the proposal "that these three individual elongated deeps constitute the 'Challenger Deep', and [we] identify them as the East, Central and West Deep. The deepest depth we obtained during the swath mapping is 10,938 metres (35,886 ft) in the West Deep (11°20.34' N, 142°13.20 E)." The depth was "obtained during swath mapping... confirmed in both N–S and E-W swaths." Speed of sound corrections were from XBT to 1,800 metres (5,900 ft), and CTD below 1,800 metres (5,900 ft).

The cross track survey of the 1999 Kairei cruise shows that the greatest depths in the eastern, central, and western depressions are 10,920 m (35,827 ft) ±10 m (33 ft), 10,894 m (35,741 ft) ±14 m (46 ft), and 10,907 m (35,784 ft) ±13 m (43 ft), respectively, which supports the results of the previous survey.

In 2002 Kairei revisited the Challenger Deep 16–25 October 2002, as cruise KR02-13 (a cooperative Japan-US-South Korea research program) with chief scientist Jun Hashimoto in charge; again with Kazuyoshi Hirata managing the ROV Kaikō team. On this survey, the size of each of the three basins was refined to 6–10 km long by about 2 km wide and in excess of 10,850 m (35,597 ft) deep. In marked contrast to the Kairei surveys of 1998 and 1999, the detailed survey in 2002 determined that the deepest point in the Challenger Deep is located in the eastern basin around 11°22.260′N 142°35.589′E, with a depth of 10,920 m (35,827 ft) ±5 m (16 ft), located about 290 m (950 ft) southeast of the deepest site determined by the survey vessel Takuyo in 1984. The 2002 surveys of both the western and eastern basins were tight, with especially meticulous cross-gridding of the eastern basin with ten parallel tracks N–S and E–W less than 250 meters apart. On the morning of 17 October, ROV Kaikō dive #272 began and recovered over 33 hours later, with the ROV working at the bottom of the western basin for 26 hours (vicinity of 11°20.148' N, 142°11.774 E at 10,893 m (35,738 ft)). Five Kaikō dives followed on a daily basis into the same area to service benthic landers and other scientific equipment, with dive #277 recovered on 25 October. Traps brought up large numbers of amphipods (sea fleas), and cameras recorded holothurians (sea cucumbers), White polychaetes (bristle worms), tube worms, and other biological species. During its 1998, 1999 surveys, Kairei was equipped with a GPS satellite-based radionavigation system. The United States government lifted the GPS selective availability in 2000, so during its 2002 survey, Kairei had access to non-degraded GPS positional services and achieved single digit meter accuracy in geodetic positioning.

The RV Melville was operated by the Scripps Institution of Oceanography

2001 – RV Melville – The 2.516-ton research vessel Melville at the time operated by the Scripps Institution of Oceanography took the Cook Expedition, Leg 6 with chief scientist Patricia Fryer of the University of Hawaii from Guam on 10 February 2001 to the Challenger Deep for a survey titled "Subduction Factory Studies in the Southern Mariana," including HMR-1 sonar mapping, magnetics, gravity measurements, and dredging in the Mariana arc region. They covered all three basins, then tracked 120 nmi (222.2 km)-long lines of bathymetry East-West, stepping northward from the Challenger Deep in 12 km (7.5 mi) sidesteps, covering more than 90 nmi (166.7 km) north into the backarc with overlapping swaths from their SeaBeam 2000 12-kHz multi-beam echosounder and MR1 towed system. They also gathered magnetic and gravity information, but no seismic data. Their primary survey instrument was the MR1 towed sonar, a shallow-towed 11/12-kHz bathymetric sidescan sonar developed and operated by the Hawaii Mapping Research Group (HMRG), a research and operational group within University of Hawaii’s School of Ocean and Earth Science and Technology (SOEST) and the Hawaii Institute of Geophysics and Planetology (HIGP). The MR1 is full-ocean-depth capable, and provides both bathymetry and sidescan data. Leg 7 of the Cook Expedition continued the MR-1 survey of the Mariana Trench backarc from 4 March to 12 April 2001 under chief scientist Sherman Bloomer of Oregon State University.

The RV Kilo Moana was used as the support ship of the HROV Nereus

2009 – RV Kilo Moana – In May/June 2009 the US Navy-owned 3,064-ton twin-hulled research vessel Kilo Moana (T-AGOR 26) was sent to the Challenger Deep area to conduct research. Kilo Moana is civilian-manned and operated by SOEST. It is equipped with two multibeam echosounders with sub-bottom profiler add-ons (the 191-beam 12 kHz Kongsberg Simrad EM120 with SBP-1200, capable of accuracies of 0.2–0.5% of water depth across the entire swath), gravimeter, and magnetometer. The EM-120 uses 1 by 1 degree sonar-emissions at the sea surface. Each 1 degree beam width sonar ping expands to cover a circular area about 192 metres (630 ft) in diameter at 11,000 metres (36,089 ft) depth. Whilst mapping the Challenger Deep the sonar equipment indicated a maximum depth of 10,971 m (35,994 ft) at an undisclosed position. Navigation equipment includes the Applanix POS MV320 V4, rated at accuracies of ½–to–2 meters. RV Kilo Moana was also used as the support ship of the hybrid remotely operated underwater vehicle (HROV) Nereus that dove three times to the Challenger Deep bottom during the May/June 2009 cruise and did not confirm the sonar established maximum depth by its support ship.

2009 – RV Yokosuka – Cruise YK09-08 brought the JAMSTEC 4,429-ton research vessel Yokosuka back to the Mariana Trough and to the Challenger Deep June–July 2009. Their mission was a two-part program: surveying three hydrothermal vent sites in the southern Mariana Trough backarc basin near 12°57’N, 143°37’E about 130 nmi northeast of the central basin of the Challenger Deep, using the autonomous underwater vehicle Urashima. AUV Urashima dives #90–94, were to a maximum depth of 3500 meters, and were successful in surveying all three sites with a Reson SEABAT7125AUV multibeam echosounder for bathymetry, and multiple water testers to detect and map trace elements spewed into the water from hydrothermal vents, white smokers, and hot spots. Kyoko OKINO from the Ocean Research Institute, University of Tokyo, was principal investigator for this aspect of the cruise. The second goal of the cruise was to deploy a new "10K free fall camera system" called Ashura, to sample sediments and biologics at the bottom of the Challenger Deep. The principal investigator at the Challenger Deep was Taishi Tsubouchi of JAMSTEC. The lander Ashura made two descents: on the first, 6 July 2009, Ashura bottomed at 11°22.3130′N 142°25.9412′E at 10,867 metres (35,653 ft). The second descent (on 10 July 2009) was to 11°22.1136′N 142°25.8547′E at 10,897 metres (35,751 ft). The 270 kg Ashura was equipped with multiple baited traps, a HTDV video camera, and devices to recover sediment, water, and biological samples (mostly amphipods at the bait, and bacteria and fungus from the sediment and water samples).

2010 – USNS Sumner – On 7 October 2010, further sonar mapping of the Challenger Deep area was conducted by the US Center for Coastal & Ocean Mapping/Joint Hydrographic Center (CCOM/JHC) aboard the 4.762-ton Sumner. The results were reported in December 2011 at the annual American Geophysical Union fall meeting. Using a Kongsberg Maritime EM 122 multi-beam echosounder system coupled to positioning equipment that can determine latitude and longitude up to 50 cm (20 in) accuracy, from thousands of individual soundings around the deepest part the CCOM/JHC team preliminary determined that the Challenger Deep has a maximum depth of 10,994 m (36,070 ft) at 11.326344°N 142.187248°E / 11.326344; 142.187248, with an estimated vertical uncertainty of ±40 m (131 ft) at two standard deviations (i.e. ≈ 95.4%) confidence level. A secondary deep with a depth of 10,951 m (35,928 ft) was located at approximately 23.75 nmi (44.0 km) to the east at 11.369639°N 142.588582°E / 11.369639; 142.588582 in the eastern basin of the Challenger Deep.