Planning, launch, and the dive phase
A realistic AUV survey mission starts well before the vehicle ever touches the water, with mission planning defining a set of waypoints or a survey pattern the vehicle will follow, along with depth targets, expected duration, and the conditions under which the vehicle should abort and return. Because there's no way to remotely correct the plan in real time once the vehicle is deep and relying on acoustic-only comms, this planning stage has to account for contingencies upfront, defining what the vehicle should do autonomously if it loses its planned track, detects an obstacle, or runs low on battery, since no one will be available to make that call for it in the moment the way an ROV operator could.
Once launched, the vehicle typically gets an initial GPS fix at the surface before diving, establishing a known starting position for its dead reckoning system. As it descends and begins its survey pattern, it starts accumulating position error through dead reckoning, using its doppler velocity log and inertial sensors to track motion relative to that last known fix. If the mission includes a surface ship, USBL positioning can supplement this by giving periodic range and bearing corrections from the ship, but for missions ranging far from any surface support, the vehicle is largely on its own between GPS fixes, executing its planned pattern purely on dead reckoning and whatever onboard sensing it uses to avoid obstacles or terrain.