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The use of battery storage systems (BSS) is an increasingly common topic in the context of the operation of various types of renewable energy sources (RES). One of the applications may be to solve the problem of energy-free operation of small hydropower plants, where quite specific requirements are placed on the design of the BSS. In the context of optimal BSS design for a given application, this paper discusses the computer analysis capabilities that are essential in the design and performance verification phase of a BSS. The paper presents the possibilities of simulation methods in the field of electrical analysis of cell current load during charging and discharging processes, thermal analysis related to the selection of a suitable cooling system with respect to the operating mode of the battery system.