Due to the stochastic nature and variability of renewable energy sources (RES), it is necessary to integrate still expensive storage capacities into an energy system with a high share of RES and to model appropriate energy market. The study presented here considers all energy carriers, however, only the electricity carrier is modeled in detail, with notion taken for the heating demand that is covered but without proper modeling of storage. A proposed two-level approach with multi-objective optimization on the global level, was used to design a Croatian Energy System (CES), where electric vehicles (EVs) are integrated to serve as battery storage in Vehicle-to-Grid (V2G) mode, for a scenario between 2015 and 2050. In addition, case study includes nine aggregated hydro power plants, one for each river basin in Croatia. Also, case study includes solar and wind power plants modeled for six locations in Croatia: Osijek, Zagreb, Rijeka, Sibenik, Split and Dubrovnik. The resulting Pareto front suggests that with assumed future costs of fuels and technology certain level of conventional energy sources will have to remain in the energy system to take into the account unfavourable weather conditions and to cover heating demand, which also results in significantly lower load factors for those power plants. Also, variants with more RES share have lower total energy system load factor and significantly higher installed capacity.