Aquatics at the 1991 Southeast Asian Games included swimming, diving and water polo events. The three sports of aquatics were held in Manila, Philippines. Aquatics events was held between 25 November to 29 November.
| 50 m freestyle |  Ang Peng Siong | 23.89 |  Richard Sam Bera | 24.24 |  Raymond Papa | 24.48 | |
| 100 m freestyle | Richard Sam Bera | 52.30 | Wisnu Warsono | 53.67 | Kenneth Yeo | 53.95 | |
| 200 m freestyle | Richard Sam Bera | 1:54.72 (rec) |  Jeffrey Ong | 1:55.97 | Albert Soetanto | 1:58.59 | |
| 400 m freestyle | Jeffrey Ong | 4:00.04 (rec) |  Ratapong Sirisanont | 4:07.32 | Pawin Kohvathana | 4:10.49 | |
| 1500 m freestyle | Jeffrey Ong | 15:50.39 | Ratapong Sirisanont | 16:18.22 | Pawin Kohvathana | 16:34.72 | |
| 100 m backstroke | David Lim Fong Jock | 58.50 | Leo Najera | 59.08 | Raymond Papa | 1:00.12 | |
| 200 m backstroke | Leo Najera | 2:10.50 | Desmond Koh Mun Kit | 2:11.19 | Dulyant Phuangthong | 2:11.26 | |
| 100 m breaststroke | Eric Buhain | 1:04.18 | Wirmandi Sugriat | Lee Patrick Concepcion | 1:05.66 | ||
| 200 m breaststroke | Lee Patrick Concepcion | 2:21.47 (rec) | Wirmandi Sugriat | 2:22.03 | Ratapong Sirisanont | 2:23.31 | |
| 100 m butterfly | Eric Buhain | 56.67 | Wisnu Warsono | 57.37 | Sabeni Sudiono | 57.59 | |
| 200 m butterfly | Eric Buhain | 2:05.10 | Tan V Meng | 2:07.50 | Niti Intharapichai | 2:09.20 | |
| 200 m individual medley | Eric Buhain | 2:06.35 | Desmond Koh Mun Kit | 2:08.36 | Tan V Meng | 2:10.73 | |
| 400 m individual medley | Eric Buhain | 4:32.66 (rec) | Ratapong Sirisanont | 4:33.51 | Desmond Koh Mun Kit | 4:33.70 | |
| 4 × 100 m freestyle relay | Indonesia | 3:32.74 | Singapore | 3:34.10 | Philippines | 3:37.34 | |
| 4 × 200 m freestyle relay | Indonesia | 7:54.31 | Thailand | 8:02.43 | Philippines | 8:07.45 | |
| 4 × 100 m medley relay | Indonesia | 3:54.66 | Singapore | 3:58.46 | Thailand | 4:09.09 | |
| 50 m freestyle | Ratiporn Wong | 27.53 | Akiko Thomson | 27.55 | Joscelin Yeo Wei Ling | 27.59 | |
| 100 m freestyle | Ratiporn Wong | 59.17 | Akiko Thomson | 59.25 | Meitri Widya Pangestika | 59.76 | |
| 200 m freestyle | Elfira Rosa Nasution | 2:07.12 | Ratiporn Wong | 2:08.55 | Meitri Widya Pangestika | 2:08.75 | |
| 400 m freestyle | Elfira Rosa Nasution | 4:25.41 | Thanya Sridama | 4:28.72 | Mudjalin Chansurb | 4:32.04 | |
| 800 m freestyle | Thanya Sridama | 9:09.70 | Theradee Tochareon | 9:13.61 | Meitri Widya Pangestika | 9:21.62 | |
| 100 m backstroke | Akiko Thomson | 1:05.00 | Praphalsai Minpraphal | 1:07.10 | Elsa Manora Nasution | 1:07.52 | |
| 200 m backstroke | Akiko Thomson | 2:20.23 | Praphalsai Minpraphal | 2:22.85 | Elsa Manora Nasution | 2:25.22 | |
| 100 m breaststroke | Sornsawan Phuvichit | 1:13.07 | Joscelin Yeo Wei Ling | 1:14.36 | Rasnin Sittart | 1:16.53 | |
| 200 m breaststroke | Sornsawan Phuvichit | 2:38.21 (rec) | Maya Masita Nasution | 2:42.64 | Rasnin Sittart | 2:43.78 | |
| 100 m butterfly | Ratiporn Wong | 1:04.95 | T. Sakulkong | 1:04.99 | May Ooi | 1:05.49 | |
| 200 m butterfly | Salline Khemcharra | 2:19.72 | Ratiporn Wong | 2:21.39 | Susanti Wangsawiguna | 2:21.75 | |
| 200 m individual medley | Elfira Rosa Nasution | 2:22.20 | Praphalsai Minpraphal | 2:25.27 | Joscelin Yeo Wei Ling | 2:25.62 | |
| 400 m individual medley | Elfira Rosa Nasution | 4:59.52 | Praphalsai Minpraphal | 5:03.64 | Maya Masita Nasution | 5:08.14 | |
| 4 × 100 m freestyle relay | Indonesia | 4:00.94 | Thailand | 4:01.45 | Singapore | 4:07.24 | |
| 4 × 100 m medley relay | Thailand | 4:25.27 | Singapore | 4:29.63 | Indonesia | 4:31.36 | |
| Men's 3 m springboard | Temmy Kusuma | 600.65 | Kristendi Permana | 593.10 | Pol Li Sohchal Ongkasing | 579.55 | |
| Men's 10 m platform | Bahri Bahriansyah | Somchai Ongkasing | Husaini Noor | ||||
| Women's 3 m springboard | Sri Muriastuti | 202.25 |  Aye Aye Soe | 187.50 | Nani Suryani Walasaki | 182.70 | |
| Women's 10 m platform | Tuti Dwi Mariastuti | Bumroongroj On Anong | Nuning Sulistyaningrum |
| Men's | Singapore | Malaysia | Philippines |