A Wrinkle in Time (Book 4) - Many Waters, by Madeleine L'Engle

A touch of computer keys, a blast of heat, and suddenly the Murry twins, Sandy and Dennys, are gasping in a shimmering desert land. If only the brothers had normal parents, not a scientist mother and a father who experiments with space and time travel. If only the Murry twins had noticed the note on the door of their mother's lab: Experiment in Progress. Please Keep Out.

But it's too late for regrets. There's a strange - and very small - person approaching, with a miniature mammoth in tow....

At last it's Sandy and Dennys's turn for an adventure - an adventure that turns serious when they discover that many waters are coming to flood the desert. The twins must find a way back home soon, or they will drown. But how will they get back to their own time? Can they?