Aquatics at the 1987 Southeast Asian Games included swimming, diving and water polo events. The three sports of aquatics were held at Senayan Swimming Stadium, Jakarta, Indonesia. Aquatics events was held between 10 September to 16 September.
| 100 m freestyle |  Ang Peng Siong | 52.34 | Oon Jin Gee | 53.13 |  Eric Buhain | 54.25 | |
| 200 m freestyle | Eric Buhain | 1:56.84 | Oon Jin Gee | 1:57.01 |  Daniel Arief Budiman | 1:58.07 | |
| 400 m freestyle |  Jeffrey Ong | 4:05.21 | Rene Concepcion | 4:10.18 | Daniel Arief Budiman | 4:11.10 | |
| 1500 m freestyle | Jeffrey Ong | 16:14.08 | Huang Ying Tsang | 16:51.65 | Martin Palacios | 17:02.59 | |
| 100 m backstroke | David Lim | 58.62 | Lukman Niode | 59.45 | Eric Buhain | 1:03.23 | |
| 200 m backstroke | David Lim | 2:06.90 | Lukman Niode | 2:10.30 | Alvin Lim | 2:10.34 | |
| 100 m breaststroke | Wirmandi Sugriat | 1:06.25 | Ng Yue Meng | 1:06.83 | Lee Patrick Concepcion | 1:06.91 | |
| 200 m breaststroke | Wirmandi Sugriat | 2:23.66 | Tjatur Sugiarto | 2:25.70 | Lee Patrick Concepcion | 2:26.03 | |
| 100 m butterfly | Eric Buhain | 56.24 | Ang Peng Siong | 56.79 | Mustamsikin | 57.76 | |
| 200 m butterfly | Eric Buhain | 2:05.34 | Willton Leo | 2:11.18 | Allen Reyes | 2:11.73 | |
| 200 m individual medley | Rene Concepcion | 2:09.86 | David Lim | 2:10.03 | Alvin Lim | 2:15.83 | |
| 400 m individual medley | Eric Buhain | 4:39.03 | Rene Concepcion | 4:46.95 | Desmond Koh | 4:51.30 | |
| 4 × 100 m freestyle relay | 3:33.36 | 3:38.42 | 3:38.65 | ||||
| 4 × 200 m freestyle relay | 7:53.73 | 7:56.86 | 8:03.64 | ||||
| 4 × 100 m medley relay | 3:54.27 | 3:56.92 | 4:04.52 | ||||
| 100 m freestyle | Nurul Huda Abdullah | 59.32 | Elfira Rosa Nasution | 1:00.44 | Yen Yen Gunawan | 1:01.43 | |
| 200 m freestyle | Nurul Huda Abdullah | 2:05.95 | Elfira Rosa Nasution | 2:08.16 | May Tan Seok Khoon | 2:11.72 | |
| 400 m freestyle | Nurul Huda Abdullah | 4:23.88 | Elfira Rosa Nasution | 4:34.90 | |||
| 800 m freestyle | Nurul Huda Abdullah | 9:12.38 |  Chatkaew Bulsuk | 9:16.36 | Kusumarn Thammongkol | 9:29.49 | |
| 100 m backstroke | Akiko Thomson | 1:06.86 | Ratna Laurentia Pradipta | 1:07.73 | Maya Masita Nasution | 1:10.46 | |
| 200 m backstroke | Ratna Laurentia Pradipta | 2:23.80 | Akiko Thomson | 2:28.35 | Papanee Jirathornwatana | 2:33.49 | |
| 100 m breaststroke | Sornsawan Phuvichit | 1:16.35 | Rainy Maria Awuy | 1:16.99 | Maturada Kunapakorn | 1:17.04 | |
| 200 m breaststroke | Sornsawan Phuvichit | 2:43.77 | Rainy Maria Awuy | 2:45.44 | Maturada Kunapakorn | 2:46.99 | |
| 100 m butterfly | Nurul Huda Abdullah | 1:04.16 | May Tan Seok Khoon | 1:05.14 | Elfira Rosa Nasution | 1:05.80 | |
| 200 m butterfly | Nurul Huda Abdullah | 2:18.74 | Elfira Rosa Nasution | 2:21.75 | May Tan Seok Khoon | 2:24.73 | |
| 200 m individual medley | Elfira Rosa Nasution | 2:23.85 | Nurul Huda Abdullah | 2:24.55 | Papanee Jirathornwatana | 2:29.32 | |
| 400 m individual medley | Nurul Huda Abdullah | 5:02.41 | Elfira Rosa Nasution | 5:03.71 | Maya Masita Nasution | 5:14.61 | |
| 4 × 100 m freestyle relay | 4:03.05 | 4:05.45 | 4:11.75 | ||||
| 4 × 100 m medley relay | 4:32.81 | 4:37.49 | 4:41.40 | ||||
| Men's 3 m springboard | Eko Setiawan | 552.42 | P. Diamadi | 481.12 | Somchai Ongkosak | 409.92 | |
| Men's 10 m platform | Eko Setiawan | 174.96 | Ongkosak Somchai | 171.57 | Doddy Wihandjito | 161.32 | |
| Women's 3 m springboard | Dwi Mariastuti | 442.23 | Sri Retno | 382.80 |  Aye Aye Soe | 381.99 | |
| Women's 10 m platform | Dwi Mariastuti | 164.94 | Indah Widyaningsih | 152.07 | Aye Aye Soe | 151.50 |
| Men's | Singapore | Indonesia | Malaysia |