According to Pearl, Dark Water is the name of the river (or creek, to be more precise) where Amiel lives. Since that's where they spend most of their time, fall in love, and even escape the fire, it's only fitting that the novel is named Dark Water, too.
The title doesn't simply reflect the name of the river, though; it's also a metaphor for what happens throughout the story. Water is nourishing and cleansing; it helps things grow and supports plants and humans alike. Yet it's also very destructive. Water can drown people or wipe out cities. In this way, water is a stand-in for love, which can help us grow and destroy us, too. We see some of both the good and bad parts of love in this book as Pearl and Amiel come together—and then fall apart.