This paper deals with scheduling the operations in systems with storage modeled as a mixed integer nonlinear program (MINLP). Due to time interdependency induced by storage, discrete control, and nonlinear operational conditions, computing even a feasible solution may require an unaffordable computational burden. We exploit a property common to a broad class of these problems to devise a decomposition algorithm related to alternating direction methods, which progressively adjusts the operations to the storage state profile. We also design a deep learning model to predict the continuous storage states to start the algorithm instead of the discrete decisions, as commonly done in the literature. This enables search diversification through a multi-start mechanism and prediction using scaling in the absence of a training set. Numerical experiments on the pump scheduling problem in water networks show the effectiveness of this hybrid learning/decomposition algorithm in computing near-optimal strict-feasible solutions in more reasonable times than other approaches.