Aquatics at the 1999 Southeast Asian Games included swimming, diving and water polo events. The three sports of aquatics were held at Hassanal Bolkiah Aquatics Center in Bandar Seri Begawan, Brunei Darussalam. Aquatics events was held between 8 August to 13 August.

Men's events

Event	Gold		Silver		Bronze
50 m freestyle	Richard Sam Bera	23.49	Wisnu Wardhana	23.71	Leslie Kwok	23.79
100 m freestyle	Richard Sam Bera	51.03	Allen Ong Hou Ming	51.73	Mark Chay	51.95
200 m freestyle	Vicha Ratanachote	1:53.43	Mark Chay	1:53.98	Sng Ju Wei	1:54.25
400 m freestyle	Dieung Manggang	4:00.34	Sng Ju Wei	4:04.55	Torwai Sethsothorn	4:05.17
1500 m freestyle	Dieung Manggang	15:57.47	Carlo Piccio	15:57.85	Steven Chandra	16:02.63
100 m backstroke	Alex Lim	56.20	Gary Tan	58.00	Felix Christiadi Sutanto	59.27
200 m backstroke	Alex Lim	2:02.09	Gary Tan	2:05.79	Felix Christiadi Sutanto	2:08.07
100 m breaststroke	Elvin Chia Tshun Thau	1:02.96	Daniel Liew	1:04.95	Non Poonchaisri	1:05.95
200 m breaststroke	Elvin Chia Tshun Thau	2:15.62	Ratapong Sirisanont	2:17.64	Muhammad Akbar Nasution	2:20.59
100 m butterfly	Albert Christiadi Sutanto	56.25	Anthony Ang	56.47	Wisnu Wardhana	56.72
200 m butterfly	Albert Christiadi Sutanto	2:02.06	Alex Lim	2:02.35	Ratapong Sirisanont	2:02.71
200 m individual medley	Ratapong Sirisanont	2:04.26	Pathunyu Yimsomruay	2:04.99	Felix Christiadi Sutanto	2:09.36
400 m individual medley	Ratapong Sirisanont	4:25.16	Albert Christiadi Sutanto	4:25.19	Torwai Sethsothorn	4:31.21
4 × 100 m freestyle relay	Indonesia	3:27.69	Singapore	3:28.12	Malaysia	3:29.62
4 × 200 m freestyle relay	Thailand	7:38.89	Singapore		Indonesia
4 × 100 m medley relay	Malaysia	3:45.61	Thailand	3:50.45	Singapore	3:55.56

Women's events

Event	Gold		Silver		Bronze
50 m freestyle	Joscelin Yeo Wei Ling	26.23	Pilin Tachakittiranan	27.01	Moe Thu Aung	27.41
100 m freestyle	Joscelin Yeo Wei Ling	56.05	Pilin Tachakittiranan	58.02	Christel Bouvron Mei Yen	58.85
200 m freestyle	Pilin Tachakittiranan	2:04.60	Christel Bouvron Mei Yen	2:06.35	Teo Mun Yee	2:09.78
400 m freestyle	Pilin Tachakittiranan	4:19.43	Christel Bouvron Mei Yen	4:21.87	Joscelin Yeo Wei Ling	4:28.59
800 m freestyle	Pilin Tachakittiranan	8:59.45	Sia Wai Yen	9:02.51	Christel Bouvron Mei Yen	9:09.99
100 m backstroke	Chonlathorn Vorathamrong	1:05.46	Elsa Manora Nasution	1:05.69	Lizza Danila	1:06.19
200 m backstroke	Chonlathorn Vorathamrong	2:20.05	Lizza Danila	2:21.57	Elsa Manora Nasution	2:23.40
100 m breaststroke	Joscelin Yeo Wei Ling	1:11.36	Kathy Echeverri	1:13.83	Siow Yi Ting	1:14.88
200 m breaststroke	Nicolette Teo	2:36.27	Tachaphorn Iamsanitamorn	2:42.90	Siow Yi Ting	2:43.56
100 m butterfly	Joscelin Yeo Wei Ling	1:00.44	Praphalsai Minpraphal	1:01.16	Moe Thu Aung	1:03.65
200 m butterfly	Praphalsai Minpraphal	2:14.54	Pilin Tachakittiranan	2:17.01	Christel Bouvron Mei Yen	2:19.71
200 m individual medley	Joscelin Yeo Wei Ling	2:17.17	Sia Wai Yen	2:20.64	Ravee Inporn Udom	2:23.99
400 m individual medley	Joscelin Yeo Wei Ling	4:51.87	Sia Wai Yen	4:52.52	Duangruthai Thammapanya	5:04.70
4 × 100 m freestyle relay	Thailand	3:53.33	Singapore	3:56.99	Indonesia	4:00.04
4 × 200 m freestyle relay	Thailand	8:25.51	Singapore	8:32.06	Indonesia	8:47.41
4 × 100 m medley relay	Thailand	4:20.76	Malaysia	4:27.07	Singapore	4:29.37

Event	Gold		Silver		Bronze
Men's 3 m springboard	Yeoh Ken Nee	582.05	Suchart Pichi	535.20	Atthain Anupan	526.05
Men's 10 m platform	Yeoh Ken Nee	577.15	Husaini Noor	519.55	Muhammad Nasrullah	497.35
Women's 3 m springboard	Farah Begum Abdullah	456.50	Leong Mun Yee	444.95	Eka Purnama Indah
Women's 10 m platform	Shenny Ratna Amelia	430.90	Tammaoros Sukruthai	420.90	Leong Mun Yee	410.70

Event	Gold	Silver	Bronze
Men's	Singapore	Philippines	Indonesia

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