This paper presents a new approach for modeling energy flows in complex energy systems with parallel supply of fresh water and electricity. Such systems consist of renewable energy sources (RES), desalination plant, conventional power plants and the residual brine storage which is used as energy storage. The presented method is treating energy vectors in the system as control variables to provide the optimal solution in terms of the lowest critical excess of electricity production (CEEP) and highest possible share of RES in the supply mix. The optimal solution for supplying the demands for fresh water and electricity is always found within the framework of model constraints which are derived from the physical limitations of the system. The presented method enables the optimization of energy flows for a larger period of time. This increases the role of energy storage when higher integration of RES in the supply mix. The method is tested on a hypothetical case of Jordan for different levels of installed wind and PV capacities, as well as different sizes of the brine storage. Results show that increasing the optimization horizon from one hour to 24 h can reduce the CEEP by 80% and allow the increase of RES in the supply mix by more than 5% without violating the CEEP threshold limit of 5%. The activity of the energy (brine) storage is crucial for achieving this goal. (C) 2015 Elsevier Ltd. All rights reserved.