You can feel the temp of the water in the bilge before pumping it out. This can sometimes point you in the right direction (i.e. hot water = engine, shower, heater, etc.; cold water = water intake, shaft coupler, rain, etc.).
If you have a hot water shower, make sure you turn off the valves in addition to the pump. This has happened to me several times where I left the valves on. The pressure from the engine pushes the water in the system without the pump even on. The faster you go, the more water pours out the shower head! And with it in the trunk it's hard to see it happening.