A reliable navigation system is a key factor for the success of an operational mission with an AUV in a real scenario. In this paper, we address the main issues involved in the implementation of a long baseline (LBL) navigation system for a REMUS AUV. This system replaces both the original hardware and software of the vehicle with a simpler, faster, less expensive and more precise system, based on a Kalman filter. We also discuss the influence of transponder location in the overall performance of the LBL navigation, and present results obtained with this new system in operational missions