The 3D scan might be good to find fish but if you want correct bathymetry you need a lot of sensors!
As Dan Erik mentioned you need correct position in x,y,z (use RTK GPS) and fast roll, pitch and heading updates.
With that in place you don't need to worry about any tidal changes since you reference to gps x,y,z and the angle to the echo will be correct.
BUT, you also need sound speed in water at the sensor (in real time) and a sound speed profile for the water column. Changes in sound speed will act exactly like a pair of glasses and "bend" the sound. If you don't compensate for this the a flat bottom will either be curved like a "smiley" or the other way around due to changes in sound speed.
To measure the sound speed profile you stop the boat.
Drop a probe (3000$) that measures the sound speed every 0.5 m and let it fall all the way to the bottom.
Upload the sound speed data from the probe to the software.
The software does ray tracing in real time for each echo to remove the refraction that the changes of sound speed does to the echoes.
This measuring must be done quite frequently, some ships use a "moving vessel profiler" that can do this without stopping the ship.
To cut it short, use single beam echo sounder to get the depth under the boat and keep the distance between the tracks short.
Use the sidescan to detect any rocks between the measuring tracks.,
If you have 100 000$ waiting to be spent, here is a shopping list in that case ;)
www.edgetech.com/product/6205s-combined-...try-side-scan-sonar/
www.valeport.co.uk/Products/Sound-Veloci...-Details/ProductID/1
Then you need a good IMU and RTK gps (L1/L2) capable is better.
Cheers
Hakan