Soil–structure interaction is a key aspect to take into account when simulating the response of civil engineering structures subjected to dynamic actions. To this end, and due to its simplicity and ease of implementation, the dynamic Winkler model has been widely used in practical engineering applications. In this model, soil–structure interaction is simulated by means of spring–damper elements. A crucial point to guarantee the adequate performance of the approach is to accurately estimate the constitutive parameters of these elements. To this aim, this article proposes the application of a recently developed parameter identification method to address such problem. In essence, the parameter identification problem is transformed into an optimization problem, so that the parameters of the dynamic Winkler model are estimated by minimizing the relative differences between the numerical and experimental modal properties of the overall soil–structure system. A recent and efficient hybrid algorithm, based on the combination of the unscented Kalman filter and multi-objective harmony search algorithms, is satisfactorily implemented to solve the optimization problem. The performance of this proposal is then validated via its implementation in a real case-study involving an integral footbridge.