Inspired by the octopus and other animals living in water, soft robots should naturally lend themselves to underwater operations, as supported by encouraging validations in deep water scenarios. This work deals with equipping soft arms with the intelligence necessary to move precisely in wave-dominated environments, such as shallow waters where marine renewable devices are located. This scenario is sub-stantially more challenging than calm deep water since, at low operational depths, hydrodynamic wave disturbances can represent a significant impediment. We propose a control strategy based on Nonlinear Model Predictive Control that can account for wave disturbances explicitly, optimising control actions by considering an estimate of oncoming hydrodynamic loads. The proposed strategy is validated through a set of tasks covering set-point regulation, trajectory tracking and mechanical failure compensation, all under a broad range of varying significant wave heights and peak spectral periods. The proposed control methodology displays positional error reductions as large as 84% with respect to a baseline controller, proving the effectiveness of the method. These initial findings present a first step in the development and deployment of soft manipulators for performing tasks in hazardous water environments.