Modern hybrid storage systems (HESS) require different storage technologies to fulfill demanding power and energy requirements. Supercapacitors (SCs) are a common component of these systems due to their excellent power capabilities. This article presents a systematic and automatic approach to identifying equivalent circuit model (ECM) parameters by using subspace system identification. Our proposed approach overcomes many of the shortcomings of previous fitting procedures, such as manual tuning, with improved results. The developed algorithms were validated through experimental tests. The resulting models, which describe the dynamic performance of the SCs, are ready to be used as building blocks in a wide range of applications, including management systems, renewable generation and electric vehicles.