Modern multibeam echo sounders (MBES), which are most widely used for collecting high-resolution bathymetry and seabed imagery, often have the capability of recording acoustic backscatter from the full water column. This capability has enabled several new applications for MBES including the study of marine organisms, the quantification of suspended sediments, imaging physical oceanographic structure, and the detection, localization, and characterization of methane gas seeps. Split-beam echo sounders (SBES) are widely used in fisheries applications, but have a similarly diverse range of other applications. Here, we review the use of both MBES and SBES systems for mapping different phenomena in the water column, with a focus on mapping methane gas seeps. In doing so, we attempt to highlight the many advantages of these systems, but also discuss some of the limitations including the masking of targets by high seafloor reverberation levels in MBES systems. We also discus some of the challenges associated with wide bandwidth SBES systems, including our attempts to maintain a frequency-independent field-of-view using constant-beamwidth transducers.