The aim of this paper is to present a development and an implementation of a tracking algorithm for Over-The-Horizon Radar (OTHR) with surface wave propagation. Proposed implementation utilizes standard tracking algorithm design for OTHR and introduces modifications of Joint Probability Data Association (JPDA) algorithm in order to simplify processing. To justify chosen approach, a simulated environment consisting of one OTHR and its corresponding targets is created and proposed implementation is tested.