The Sea of Always / Jodi Lynn Anderson.

Enhanced descriptions from Syndetics:

Perfect for fans of Newbery winner The Girl Who Drank the Moon , the "inventive, bewitching" ( Kirkus Reviews ) second book in the haunting and magical New York Times bestelling Thirteen Witches series from Jodi Lynn Anderson follows Rosie as she hunts the remaining witches.

After twelve-year-old Rosie Oaks's triumph over a powerful evil witch, a whole new world opened up to her--one full of witches who control many of the experiences that make life worth living and use their dominion to torment people. As the latest in a line of powerful witch hunters, it's up to Rosie to defeat them. With her loyal friend Germ by her side and her newly created witch-weapon at the ready, Rosie leaves home on a quest to find and vanquish the remaining of the original Thirteen Witches.

With the help of an enchanted time-traveling whale, Rosie travels through the depths of the sea and across vast distances as she seeks to fulfill her destiny. The lives of those she loves hang in the balance and her skills are put to the ultimate test as Rosie digs deep for the strength to complete her quest. But can one girl truly hope to eliminate forces that have been at work for centuries?