The Sheffield 23-year-old from, now based in New Zealand, took gold in her second British record of the day as she touched in 31.40 seconds, 0.9sec ahead of her principal rival, Agnes Kovacs of Hungary.
Baker was gaining revenge for her narrow defeat by Kovacs at the European Championships in Istanbul last summer.
"It was very nice to beat Agnes because she won at Istanbul," she said. "I prefer long-course championships because I don't like turns, but this was very good. I had a slow turn - in fact an awful turn - and that probably cost me a European record. But I'd rather have a gold medal than a European record."
Margaretha Pedder was also in record form, the Portsmouth swimmer breaking her own British mark in the women's 200m butterfly final. Pedder finished fifth in 2min 9.56sec.
Ed Sinclair finished fourth in the 200m freestyle final, again in a British record time. James Hickman qualified for today's 100m butterfly final. Sue Rolph qualified second-fastest for the 100m freestyle final, while Katy Sexton and Sarah Price reached the 100m backstroke final.