A team of scientists from the USGS Upper Midwest Environmental Science Center in La Crosse, Wisconsin, is studying ways to control and deplete aquatic invasive species in the Upper Mississippi River System (UMRS). One study site included a select backwater on the Marseilles Pool in the Illinois River. Split-beam hydroacoustic (stationary and mobile, 200-kHz transducers), side-scan sonar imagery, and bathymetry data were collected and integrated to evaluate fish abundance and distributions in specific areas before, during, and after integrated pest management tools were applied to deplete localized populations of invasive Asian carp. The images created with sonar and bathymetry data were georeferenced and mosaicked to create an underwater picture of the backwater bottom to delineate specific zone areas and calculate water volumes within those zones. The ultimate goals of this backwater mapping application will be used to help calculate the relative abundance of aquatic invasive species in specific areas at specific time points and help place attractant or deterrent technologies in specific locations for the control and depletion of unwanted invasive species.