A method for rapidly and relatively inexpensively mapping oyster bottom is described. The method uses an acoustic profiler to differentiate substrate type, a fathometer to assess bottom relief and a global positioning system to accurately establish position. The method has the following desirable traits: use from a small research vessel, usable in most weather conditions, requires only a two-person crew, rapidly discriminates bottom type while underway, usable in shallow (<1 m) or deep (>10 m) water, accurate and precise navigation. The method has been used successfully to map the oyster reefs and oyster bottom of Galveston Bay, Texas, USA an area of approximately 1000 km super(2)