System and method for navigating an unmanned undersea vehicle (UUV) using three-dimensional acoustic reflectivity data sets and a beam steered downward looking sonar capturing sub-bottom features and creating three-dimensional representations to compare with the reflectivity data sets to general navigation corrections. Acoustically senses and exploits sub-bottom features for navigation of UUVs that can provide more reliable navigation than using surface features alone, since much of the sea floor is flat (e.g. on continental shelves and abyssal plains).