Van den Hoogenband won his heat in one minute 45.09 seconds, easing off in the second half of the race. Lithuania's Saulius Binevicius was the fastest qualifier for the evening's final, 0.01 seconds faster than the Dutchman.
Van den Hoogenband won Saturday's 100 freestyle in 46.81 seconds, falling a mere 0.07 seconds short of the world short-course mark set back in 1994 by Russia's Alexander Popov, whom he toppled as Olympic champion in 2000.
Dutch team mate Marleen Veldhuis led the way in the women's 50 metres freestyle heats in 24.74 but faced a strong challenge in the final session from Germany's Sandra Voelker, newly crowned 100 freestyle champion Malia Metella of France and Alison Sheppard of Britain, who is defending her title.
VDH steers Dutch to relay world record
Veldhuis also claimed a place in the 200 freestyle final as third-fastest overall qualifier behind British pace-setter Melanie Marshall, who clocked 1:55.31.
Britain's Ian Edmond set a championship record of 2:07.38 in the men's 200 metres breaststroke heats. Second-fastest final qualifier was team mate James Gibson, who won the 100 breaststroke on Friday.
Russia's Stanislava Komarova, the European long-course champion, led the way in the 200 backstroke in 2:06.67.
Commonwealth and defending champion Sarah Price was second overall in 2:07.02 but fellow Briton Katy Sexton, the world long-course champion, did not compete, having returned home early with a viral illness.
Hungary's Eva Risztov, who retained her 200 metres butterfly title on Thursday, aimed for a second gold in the 400 individual medley, having qualified second-fastest overall for the final behind Russia's Yana Tolkacheva.
European record for Britain's Edmond
VDH flirts with 100m freestyle world record