Aquatics at the 1989 Southeast Asian Games included swimming, diving and water polo events. The three sports of aquatics were held in Kuala Lumpur, Malaysia. Aquatics events was held between 23 August to 27 August.
| 50 m freestyle | 23.27 | 24.46 | Shared silver | ||||
| 100 m freestyle |  Richard Sam Bera | 52.19 |  Ang Peng Siong | 52.53 | Mustamsikin | 54.96 | |
| 200 m freestyle | David Lim | 1:55.93 | Oon Jin Gee | 1:56.34 |  Eric Buhain | 1:56.62 | |
| 400 m freestyle |  Jeffrey Ong | 4:03.25 | Richard Sam Bera | 4:05.40 | Martin Palacios | 4:10.25 | |
| 1500 m freestyle | Jeffrey Ong | 15:56.23 | Martin Palacios | 16:56.28 | Desmond Koh | 17:22.91 | |
| 100 m backstroke | David Lim | 58.87 | Irving Ng | 1:02.20 |  Nopporn Chaoprasert | 1:02.80 | |
| 200 m backstroke | David Lim | 2:09.85 | Tan V Meng | 2:13.15 |  Maung Maung Win | 2:17.58 | |
| 100 m breaststroke | Ng Yue Meng | 1:05.28 | Wirmandi Sugriat | 1:05.48 | Lee Chee Keen | 1:07.01 | |
| 200 m breaststroke | Wirmandi Sugriat | 2:23.82 | Lee Chee Keen | 2:24.32 | Tjatur Sugiarto | 2:25.72 | |
| 100 m butterfly | Ang Peng Siong | 56.00 | Eric Buhain | 56.41 | Mustamsikin | 57.01 | |
| 200 m butterfly | Eric Buhain | 2:04.02 | Tan V Meng | 2:06.60 | Desmond Koh | 2:07.69 | |
| 200 m individual medley | Eric Buhain | 2:06.94 | David Lim | 2:10.77 | Wirmandi Sugriat | 2:11.85 | |
| 400 m individual medley | Eric Buhain | 4:35.35 | Desmond Koh | 4:37.25 | Tan V Meng | 4:40.43 | |
| 4 × 100 m freestyle relay | Singapore | 3:32.81 | Indonesia | 3:36.61 | Philippines | 3:40.00 | |
| 4 × 200 m freestyle relay | Singapore | 7:54.18 | Philippines | 8:01.20 | Indonesia | 8:04.11 | |
| 4 × 100 m medley relay | Singapore | 3:52.89 | Indonesia | 3:59.54 | Philippines | 4:01.54 | |
| 50 m freestyle | Akiko Thomson | 27.62 | Thanyaluk Sakulkong | 28.17 | Yustina Atmaja Yen Yen Gunawan | 28.58 | |
| 100 m freestyle | Akiko Thomson | 59.27 | Nurul Huda Abdullah | 1:00.04 | May Tan Seok Khoon | 1:00.52 | |
| 200 m freestyle | Nurul Huda Abdullah | 2:05.75 | May Tan Seok Khoon | 2.08.95 | Elfira Rosa Nasution | 2:09.55 | |
| 400 m freestyle | Nurul Huda Abdullah | 4:21.58 | Elfira Rosa Nasution | 4:29.75 | Thanya Sridama | 4:30.28 | |
| 800 m freestyle | Nurul Huda Abdullah | 9:06.67 | Thanya Sridama | 9:11.62 | Anchalee Hoprasatsuk | 9:33.38 | |
| 100 m backstroke | Akiko Thomson | 1:06.47 | Ratna Laurentia Pradipta | 1:07.77 | Chan Peck Hong | 1:10.24 | |
| 200 m backstroke | Nurul Huda Abdullah | 2:23.65 | Akiko Thomson | 2:24.01 | Ratna Laurentia Pradipta | 2:25.47 | |
| 100 m breaststroke | Sornsawan Phuvichit | 1:15.89 | Maturada Kunapakorn | 1:17.02 | Jong Su Ting | 1:17.43 | |
| 200 m breaststroke | Sornsawan Phuvichit | 2:42.10 | Jong Su Ting | 2:44.26 | May Ooi | 2:44.72 | |
| 100 m butterfly | May Tan Seok Khoon | 1:04.05 | Nurul Huda Abdullah | 1:04.81 | Elfira Rosa Nasution | 1:05.39 | |
| 200 m butterfly | Nurul Huda Abdullah | 2:18.76 | May Tan Seok Khoon | Elfira Rosa Nasution | |||
| 200 m individual medley | Nurul Huda Abdullah | 2:22.74 | Elfira Rosa Nasution | 2:23.44 | May Ooi | 2:29.21 | |
| 400 m individual medley | Nurul Huda Abdullah | 4:59.61 | Elfira Rosa Nasution | 5:05.37 | Thanya Sridama | 5:09.12 | |
| 4 × 100 m freestyle relay | Indonesia | 4:02.06 | Thailand | 4:03.85 | Singapore | 4:08.77 | |
| 4 × 100 m medley relay | Malaysia | 4:28.94 | Indonesia | 4:29.98 | Thailand | 4:33.32 | |
| Men's 3 m springboard | Kristendi Permana | 550.20 | Kris Darmakusuma | 545.30 | Somchai Omkasing | 533.75 | |
| Men's 10 m platform | Somchai Omkasing | 493.45 | Eko Setiawan Loeloes | 481.90 | Sugeng Riyadi | 439.30 | |
| Women's 3 m springboard | Dwi Mariastuti | 378.90 | Sri Retno Ardiani | 346.40 | Aye Aye Soe | 342.10 | |
| Women's 10 m platform | Dwi Mariastuti | 338.65 | Aye Aye Soe | 305.82 | Thuzar Aye | 301.35 |
| Men's | Singapore | Malaysia | Indonesia |