Seamonkey runs a small embedded computer to handle all of its onboard processing. This computer directly communicates with the sensor devices to collect data. Using the information such as how quickly it's moving, where sounds are coming from underwater, and what stage the vehicle is in its mission, the computer's control and navigation loops determine the appropriate speeds that each of the motors should turn in order for the vehicle to reach its desired position.

A fiberoptic tether on the vehicle allows a remote dockside computer to monitor the vehicle during testing. The software structure allows the vehicle to be run completely remotely from the dockside station for debugging and testing.