Aquatics at the 1965 Southeast Asian Peninsular Games included swimming, diving, and waterpolo events. The sports of aquatics were held at Kuala Lumpur, Malaysia. Aquatics events was held between 15 December to 18 December.
| 100 m freestyle |  Tan Thuan Heng | 57.9 (rec) |  Tieng Sok | 58.5 |  Somchai Limpichat | 1:00.3 | |
| 200 m freestyle | Tan Thuan Heng | 2:07.9 | Tin Maung Ni | 2:10.5 | Tieng Sok | 2:14.1 | |
| 400 m freestyle | Tan Thuan Heng | 4:33.4 | Tin Maung Ni | 4:33.7 |  Chan Chee Seng | 4:52.2 | |
| 1500 m freestyle | Tin Maung Ni | 18:17.6 | Tan Thuan Heng | 18:54.6 | Chan Chee Seng | 19:46.4 | |
| 100 m backstroke | Michael Eu | 1:07.9 | Alex Chan | 1:10.2 | Hem Thon | 1:11.4 | |
| 200 m backstroke | Michael Eu | 2:30.7 | Hem Thon | 2:33.5 | Alex Chan | 2:33.6 | |
| 100 m breaststroke | Phath Sam Onn | 1:15.6 | Mak Om | 1:16.7 | Somchai Purchaipaew | 1:17.4 | |
| 200 m breaststroke | Phath Sam Onn | 2:48.8 | Somchai Purchaipaew | 2:50.9 | Chong Teck Cheng | 2:51.3 | |
| 100 m butterfly | Bernard Chan | 1:04.5 (rec) | Maung Nyan | 1:05.2 | Var Nay Oeun | 1:05.6 | |
| 200 m butterfly | Vichian Magtanaroong | 2:31.0 | Alex Chan | 2:31.4 | Narong Chokumnuay | 2:32.6 | |
| 400 m individual medley | Tan Thuan Heng | 5:25.1 | Narong Chokumnuay | 5:30.5 | Nanda Kyaw Zwa | 5:35.2 | |
| 4 × 200 m freestyle relay | Thailand Somchai Limpichat Anant Pleanboonlers Narong Chokumnuay Duang Kongcharon | 9:07.5 (rec) | Singapore | 9:11.9 | Cambodia | 9:12.1 | |
| 4 × 100 m medley relay | Singapore Michael Eu Kenneth Kee Keng Siong Beng Tan Thuan Heng | 4:28.3 | Cambodia | 4:30.1 | Thailand | 4:35.4 | |
| 100 m freestyle | Patricia Chan | 1:08.8 | Jovina Tseng | 1:11.1 | Nguyen Thi Tuyet Van | 1:12.9 | |
| 200 m freestyle | Patricia Chan | 2:36.3 | Molly Tay | 2:38.1 | Sally Soe | 2:42.6 | |
| 400 m freestyle | Patricia Chan | 5:28.3 | Mary Soe | 5:48.6 | Molly Tay | 5:55.0 | |
| 100 m backstroke | Chuon Kun | 1:18.7 | Molly Tay | 1:19.0 | Jovina Tseng | 1:19.6 | |
| 200 m backstroke | Chuon Kun | 2:49.4 | Molly Tay | 2:52.6 | Jovina Tseng | 2:58.9 | |
| 100 m breaststroke | Chintana Thongratana | 1:27.3 | Umbhai Inphang | 1:30.1 | Pech Vanna | 1:30.8 | |
| 200 m breaststroke | Chintana Thongrat | 3:06.3 | Pech Vanna | 3:09.4 | Polly Ba San | 3:13.5 | |
| 100 m butterfly | Patricia Chan | 1:14.3 | Jovina Tseng | 1:14.8 | Mya Mya Win | 1:23.4 | |
| 200 m butterfly | Patricia Chan | 2:53.9 | Jovina Tseng | 2:57.5 | Mya Mya Win | 3:08.6 | |
| 200 m individual medley | Patricia Chan | 2:52.9 | Jovina Tseng | 2:58.3 | Chuon Kun | 3:02.1 | |
| 4 × 100 m freestyle relay | Singapore Jovina Tseng Tay Chin Joo Nora Tay Patricia Chan | 4:58.4 (rec) | Cambodia | 5:14.2 | 5:15.8 | ||
| 4 × 100 m medley relay | Singapore | 5:27.9 | Cambodia | 5:35.1 | 5:42.5 | ||
| Men's springboard | Hui Peng Seng | 140.53 pts | S. Oonsanit | 127.56 | Chaowalit Limtrakul | 124.07 |
| Men's highboard | Chaowalit Limtrakul | 94.44 pts | Suthi Panitchareonnam | 87.65 | Chan Peng Kuang | 82.33 |
| Women's springboard | Verachit Tungkitsuk | 86.97 pts | Nora Tay | 84.98 | ||
| Women's highboard | Verachit Tungkitsuk | 42.92 pts | ||||
| Men's water polo | Singapore | Malaysia | Thailand |