In addition to processing bathymetric data, my research on lakes requires sub-bottom profiling, or the collection of low-energy seismic data collected similarly to bathymetric data. The system we use is the SyQwest HydroBox, which, due to many hardware and software limitations, has been particularly frustrating. Still, when it does work properly, the HydroBox data has been invaluable to our lakes research. Unfortunately, the software supplied with the HydroBox is not particularly good at visualizing the collected data after collection.
A few months ago I needed to create detailed bathymetric maps for a water utility with which I was doing research. Our usual approach is to use an old Windows XP laptop with a serial port to log data from our Garmin GPS/Depth sounder unit. On the laptop, we used sofware called UnderSee Explorer (formerly Contour3D) which as far as I can tell, is now completely out of business. Usually the lakes we do research on are quite small, and the battery life of our laptops (around a few hours) is not an issue.