The speed of sound in water is proportional to temperature and conductivity — which are approximately dynamic functions of water column depth and temperature (and time depending on the properties of the region you are in — the tenperature can change a lot over short time scales). You need to measure to measure these properties in order to obtain a sufficiently accurate sound speed profile to be able to trace the path taken by acoustic energy projected from the transceiver, off the sea floor and back to the transceiver. Inaccurate sound velocity quickly becomes one of the largest error terms in measurement accuracy. We computed sound speed profiles as often as we reasonably could — sometimes the science objective involved measuring these properties and we’d use data from those measurements but sometimes we were just transiting along and would draw from a supply of expendable bathy thermographs that we could use to make sound speed profiles periodically (but certainly not often enough to maintain accurate calibration all the time.)
The ship is moving and the orientation of the array needs to be accurately calibrated — shipboard MRUs are expensive and imperfect.
The water column is rising and falling and vertical position measurement accuracy is very low from systems like gps compared to horizontal measurement accuracy.
The ship is pitching and with many ship designs this can create bubbles which can be swept beneath the ship — a small amount of bubbles close to the transceiver head can absolutely overwhelm the noise budget of these systems.
I’d be curious to know how much data from ship mounted sonar systems are actually useable for large scale high resolution mapping. I believe the best teams that build high resolution global sea floor maps rely on satellite gravimetric measurements for baselines — and use very sophisticated algorithms to fuse shipboard datasets with the global gravimetry — which im guessing probably have to throw away huge amounts of information from the higher resolution shipboard systems ...