Many of the problems of operating an AUV can be reduced to one of navigation: How accurately do you know where you are. Navigational precision determines the ability to follow track liens,the ability to map a target to world coordinates, and ultimately, even determines the areas where you are willing to operate the vehicle. This paper presents the technique used for long baseline acoustic navigation by REMUS, a low cost AUV developed by the Oceanographic Systems Laboratory of the Woods Hole Oceanographic Institution. Adapting the traditional long base line approach to this vehicle presents a complex problem because it must be low power, low cost, and small in size, and in addition must work in a shallow water environment. The REMUS system uses a single data acquisition system and DSP to interrogate and receive multiple transponders in a sequential manner. It uses spread spectrum technology which reduces the impact of multi-path in the shallow water environment. A moored pair of acoustic transponders whose coordinates are determined using differential or P-Code GPS allow the vehicle to navigate in world coordinates. The DSP minimizes the hardware requirements, thus lowering the associated hardware cost, size, and complexity. This paper describes the techniques used and provides result of this system using frequencies in the 20-30 khz band, giving a range of up to 1500 meters in water 4 meters deep, and also 10-15 khz band, giving a range of up to 7000 meters in waters 14 meters deep.