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.

Men's events

Event	Gold		Silver		Bronze
50 m freestyle	Ang Peng Siong	23.27	Richard Sam Bera	24.46	Shared silver
			Harold Gan
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

Women's events

Event	Gold		Silver		Bronze
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

Event	Gold		Silver		Bronze
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

Event	Gold	Silver	Bronze
Men's	Singapore	Malaysia	Indonesia