A method and a controller unit (110) for controlling motion of a watercraft (120) with a hydrofoil (130) are disclosed. The controller unit (110) obtains (A010) information indicating shape of water surface in front of the hydrofoil (130). The controller unit (110) further predicts (A040) wave acceleration of the watercraft (120) using a neural network. Furthermore, the controller unit (110) determines a target route and corresponding total acceleration of the watercraft (120) under a set of constraints. The total acceleration is minimized when the watercraft (120) travels according to the target route. The set of constraints includes: a first constraint that the hydrofoil (130) stays within an interval relative to the water surface, and a second constraint relating to magnitude of acceleration derived from maximum AoA and the predicted wave acceleration. The controller unit (110) calculates an AoA for the target route. Next, the controller unit (110) sends a signal for adjusting the hydrofoil (130) according to the AoA. A corresponding computer program (403) and a computer program carrier (405) are also disclosed.