How many times has this happened, just once or can you repeat the issue multiple times by filling it up and running the boat only to find it empty again?
Have you had the coolant changed recently? Could just be the engine cooling system burping and clearing the air bubbles during the first run after this service. If so this is normal, just fill it back up and go.
If it is a repetitive problem the coolant has got to be going somewhere. The engine could be burning it (head gasket, cracked head, etc.) or it is leaking (either internally to the boat or outside the boat into the water). A pressure test to the cooling system should help you track down the issue.