Aquatics at the 1969 Southeast Asian Peninsular Games included swimming, diving, and waterpolo events. The sports of aquatics were held in Rangoon, Burma. Aquatics events was held between 10 December to 13 December.

Men's events

Event	Gold		Silver		Bronze
100 m freestyle	Tan Thuan Heng	57.4	Ohn Thwin		Nanda Kyaw Zwa
200 m freestyle	Tan Thuan Heng	2:06.4	Ohn Thwin	2:10.2	Lim Cheik Sung	2:13.6
400 m freestyle	Tan Thuan Heng	4:38.6	Lim Cheik Sung	4:45.1	Poh Thaw Dar	4:45.6
1500 m freestyle	Alex Chan	19:02.1	Roy Chan	19:08.6	Lim Cheik Sung	19:16.7
100 m backstroke	Alex Chan	1:06.8	Roy Chan	1:08.6	Ohn Thwin	1:08.9
200 m backstroke	Alex Chan	2:27.8	Roy Chan	2:29.1	Nanda Kyaw Zwa
100 m breaststroke	Maung Kyi	1:15.4	Somchai Purgchaipaew	1:16.3	Joseph Yow	1:17.1
200 m breaststroke	Somchai Purgchaipaew		Joseph Yow	2:52.0	Phone Myat Thu	2:52.7
100 m butterfly	Nanda Kyaw Zwa	1:02.3	Aung Hlain Win		Vichian Magtanaroong
200 m butterfly	Nanda Kyaw Zwa	2:21.3	Alex Chan	2:21.5	Vichian Magtanaroong
400 m individual medley	Alex Chan	5:12.2	Roy Chan	5:19.4	Nanda Kyaw Zwa	5:24.3
4 × 100 m freestyle relay	Singapore	3:54.9	Burma	3:55.4	Thailand	4:02.1
4 × 200 m freestyle relay	Singapore	8:45.8	Burma	8:47.7	Thailand	9:25.2
4 × 100 m medley relay	Burma	4:18.1	Singapore	4:19.6	Thailand	4:20.8

Women's events

Event	Gold		Silver		Bronze
100 m freestyle	Patricia Chan	1:05.9	Tay Chin Joo	1:07.5	Marlar	1:08.7
200 m freestyle	Patricia Chan	2:25.6	Marlar	2:31.3	Molly Tay Chin Say	2:31.3
400 m freestyle	Patricia Chan	5:01.7	Sidney M. Keenan	5:14.6	Marlar	5:24.8
100 m backstroke	Patricia Chan	1:13.9	Molly Tay Chin Say	1:17.8	Ong Mei Lin	1:18.2
200 m backstroke	Patricia Chan	2:38.9	Molly Tay Chin Say	2:49.0	Ong Mei Lin	2:49.6
100 m breaststroke	Chintana Thongratana	1:24.6	Esther Tan	1:26.8	Polly Ba San
200 m breaststroke	Chintana Thongratana		Polly Ba San		Esther Tan	3:07.2
100 m butterfly	Patricia Chan	1:11.4	Tay Chin Joo	1:14.8	Ong Mei Lin	1:20.0
200 m butterfly	Patricia Chan	2:39.1	Tay Chin Joo	2:51.7	Ong Mei Lin	3:04.2
200 m individual medley	Patricia Chan	2:40.0	Tay Chin Joo	2:50.0	Ong Mei Lin	2:51.8
4 × 100 m freestyle relay	Singapore	4:38.5	Burma	4:40.3	Thailand	5:20.0
4 × 100 m medley relay	Singapore	5:01.8	Burma	5:11.1	Thailand	5:19.4