"Sixty people were arrested for demonstrating in unauthorised areas, and 30 for disturbing the peace," during the children-oriented procession attended by thousands and broadcast live on national television, police spokeswoman Yvette Verboon told AFP.
"Arrests were made on both sides," Verboon said amid an increasingly acrimonious and racially-charged debate in the Netherlands.
State broadcaster NOS showed images of minor scuffles breaking out on the main square, where Saint Nicholas appeared on a balcony, with protesters unfurling a large banner reading "Black Pete Racism".
"Everyone can talk about Black Pete's colour but you can't disturb a children's party like that," he told NOS.
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Gouda mayor Milo Schoenmaker said the atmosphere had been "vicious".
"It's a pity that adults from outside the city felt the need to demonstrate among the children at the end of the procession," national news agency ANP quoted Schoenmaker as saying.
Public prosecutor spokesman Wouter Bos said all those held for demonstrating in the wrong place were anti-Black Pete protesters and they would be fined 220 euros ($275) each.
The fate of those arrested for public disorder offences "will be decided later," he said.
Many say that Pete -- traditionally dressed in a gaudy medieval costume with a blackened face, red lips and an afro wig -- is a racist stereotype dating from the colonial era.
Black Pete's defenders say he is black from coming down the chimney and refuse to admit there might be anything racist about the historic character.