Double Paralympic champion Maisie Summers-Newton also claimed gold in the SM6 200m individual medley, while Bruce Dee won silver in the same men’s event.
“My main goal is to break the world record soon,” said Winnifrith after her victory.
“I’m breaking my personal best quite a lot now so it’s just going to be about keeping going with my training and hopefully get nearer to that.”
Winnifrith, who had already achieved the event’s qualifying time for the Paris Paralympics at the Aquatics GB Swimming Championships this month, finished ahead of neutral athlete Mariia Pavlova and Nahia Borezzo Zudaire of Spain.
On Monday, Mark Tompsett won gold and William Ellard silver in the men’s S14 100m backstroke, while there were also silvers for Grace Harvey in the women’s S6 100m freestyle and Megan Neave in the women’s S14 100m backstroke.
The championships are the last major international test before this summer’s Paris Paralympics, and it is also open to non-European swimmers.