Can I safely run the microwave for an extended time with just a bowl of water? I would like to leave a microwave running for several minutes (2-5, the longer the better) as part of a research project (I'm measuring the microwave emissions). 

Is it safe to put a bowl of water in the microwave to prevent the magnetron from overheating? If not is there something else I could put in.

To answer the obvious question, I do not want to put food in the microwave because I intend to be running the microwave frequently, and it is not sustainable to buy a frozen pizza every time I want to run the microwave.
Sure you can - heating water is essentially what microwaves are built for. They heat food by heating the water inside. So skip the pizza and use plain old tap water.

You want to take two small precautions, though:  


Use a microwave-safe container, e.g. a heat-proof glass or porcelain bowl.
Take precautions against overheating - a small stone or toothpick should do the trick.