Aquatics at the 2001 Southeast Asian Games included swimming, Synchronized swimming, diving and water polo events. The three sports of aquatics were held in Kuala Lumpur, Malaysia. Aquatics events was held between 10 September to 18 September.
| 50 m freestyle |  Richard Sam Bera | 23.03 |  Arwut Chinapasaen | 23.36 |  Allen Ong Hou Ming | 23.55 | |
| 100 m freestyle | Richard Sam Bera | 51.03 | Allen Ong Hou Ming | 51.31 |  Mark Chay Jung Jun | 51.76 | |
| 200 m freestyle | Mark Chay Jung Jun | 1:52.67 | Dulyarit Phuangthong | 1:52.87 | Sng Ju Wei | 1:54.33 | |
| 400 m freestyle | Torwai Sethsothorn | 3:58.18 |  Miguel Mendoza | 3:59.75 | Dieung Anak Manggang | 4:00.12 | |
| 1500 m freestyle | Torwai Sethsothorn | 15:49.72 | Miguel Mendoza | 15:54.00 | Dieung Anak Manggang | 15:55.73 | |
| 100 m backstroke | Alex Lim | 56.16 | Dulyarit Phuangthong | 57.71 | Gary Tan | 57.89 | |
| 200 m backstroke | Alex Lim Keng Liat | 2:02.91 | Gary Tan | 2:06.10 | Gerald Koh | 2:07.01 | |
| 100 m breaststroke | Elvin Chia | 1:03.15 | Tran Xian Hien | 1:04.94 | Muhammad Akbar Nasution | 1:06.04 | |
| 200 m breaststroke | Elvin Chia Tshun Thau | 2:18.40 | Muhammad Akbar Nasution | 2:22.82 | Tran Xian Hien | 2:23.48 | |
| 100 m butterfly | Anthony Ang | 55.40 | Allen Ong Hou Ming | 55.72 | Gan Wei Ming | 56.38 | |
| 200 m butterfly | Anthony Ang | 2:01.84 | Gan Wei Ming | 2:05.14 | Dieung Manggang | 2:05.70 | |
| 200 m individual medley | Dulyarit Phuangthong | 2:05.75 | Miguel Molina | 2:06.25 | Phatunyu Yinsomruay | 2:07.38 | |
| 400 m individual medley | Torwai Sethsothorn | 4:29.43 | Juan Carlo Piccio | 4:30.31 | Phatunyu Yinsomruay | 4:32.29 | |
| 4 × 100 m freestyle relay | Singapore | 3:27.49 | Indonesia | 3:31.01 | Thailand | 3:39.38 | |
| 4 × 200 m freestyle relay | Singapore | 7:38.82 | Thailand | 7:39.76 | Philippines | 7:41.17 | |
| 4 × 100 m medley relay | Malaysia | 3:46.29 | Singapore | 3:51.36 | Indonesia | 3:52.91 | |
| 50 m freestyle |  Moe Thu Aung | 26.34 | Joscelin Yeo Wei Ling | 26.41 | Jacqueline Lim Kim Tor | 26.79 | |
| 100 m freestyle | Joscelin Yeo Wei Ling | 57.13 | Moe Thu Aung | 57.61 | Pilin Tachakittiranan | 58.69 | |
| 200 m freestyle | Pilin Tachakittiranan | 2:04.70 | Chorkaew Choompol | 2:05.98 | Siripiya Sutanto | 2:07.24 | |
| 400 m freestyle | Ravee Intporn-Udom | 4:24.53 | Pilin Tachakittiranan | 4:24.73 | Sia Wai Yen | 4:24.87 | |
| 800 m freestyle | Ravee Intporn-Udom | 9:02.84 | Sia Wai Yen | 9:03.00 | Pornrada Srisawat | 9:10.96 | |
| 100 m backstroke | Chonlathorn Vorathamrong | 1:03.93 | Maria Lizza Danila | 1:05.10 | Chorkaew Choompol | 1:07.34 | |
| 200 m backstroke | Chonlathorn Vorathamrong | 2:19.82 | Maria Lizza Danila | 2:23.47 | Sia Wai Yen | 2:23.87 | |
| 100 m breaststroke | Nicholette Teo Wei Min | 1:12.64 | Jenny Rose Guerero | 1:12.91 | Siow Yi Ting | 1:13.69 | |
| 200 m breaststroke | Siow Yi Ting | 2:31.90 | Nicholette Teo Wei Min | 2:35.01 | Jenny Rose Guerero | 2:36.05 | |
| 100 m butterfly | Joscelin Yeo Wei Ling | 1:01.16 | Moe Thu Aung | 1:01.76 | Pilin Tachakittiranan | 1:03.69 | |
| 200 m butterfly | Christel Bouvron Mei Yen | 2:17.37 | Pilin Tachakittiranan | 2:19.62 | Tachaphorn Iamsanitamorn | 2:20.64 | |
| 200 m individual medley | Joscelin Yeo Wei Ling | 2:19.76 | Siow Yi Ting | 2:21.80 | Sia Wai Yen | 2:22.44 | |
| 400 m individual medley | Sia Wai Yen | 4:55.87 | Ravee Intporn-Udom | 5:03.00 | Jenny Rose Guerero | 5:08.09 | |
| 4 × 100 m freestyle relay | Thailand | 3:54.11 | Singapore | 3:54.75 | Malaysia | 4:03.38 | |
| 4 × 200 m freestyle relay | Thailand | 8:32.07 | Singapore | 8:38.73 | Malaysia | 8:45.14 | |
| 4 × 100 m medley relay | Thailand | 4:22.01 | Singapore | 4:23.41 | Philippines | 4:23.74 | |