System and method for generating vehicle position fixes for an underwater vehicle based on images of a target object on the seafloor. The position of the target object is estimated based on a selected pixel on the target. For each image of the target, there is a different selected pixel, and a different uncertainty associated with the target location based on the selected pixel. Vehicle position fixes for the underwater vehicle are computed based on an analysis of the selected pixels for each target, the uncertainties of the selected pixel positions, the location and uncertainty of location of the vehicle collecting the pixel positions, and other information collected about the target.