Vision based motion estimation algorithms are widely used in ground-based and aerial robotics. Combined with inertial measurement units, they have proven to be a precise and low-cost sensor for velocity and pose estimation. In this paper we show that stereo vision based odometry can be used by autonomous underwater vehicles (AUV) that navigate close to the seabed for velocity and incremental pose estimation in small areas. We present the integration of two different stereo visual odometry algorithms into an AUV and experiments carried out in laboratory and harbour conditions comparing vision based pose estimates with ground truth.