Subbottom profiling is used in Florida underwater archaeology extensively. It is a effective method of mapping underwater sinkholes, caves and their existing geomorphology. The sound signal is transmitted vertically with a strong signal and low frequency. Some signals reflect off of bedrock and others penetrate into the floor. Hydrophones aboard the ship record the reflected signals. The resulting data determines the stratigraphy of the sediments and bedrock, and also the profile of given structures. For example, it can provide information about the profile of a sinkhole.
Following is an example of a subbottom profiler:
Photo is Courtesy of NOAA OceanExplorer
subbottom profiler NOAA webpage: http://oceanexplorer.noaa.gov/projects/02lewis/perspective/media/subbtm.html