Can I submit just two great letters of recommendation if the application calls for three? I'm getting ready to apply for a graduate program in biophysics at a few different universities. I'd just like to ask a question regarding the quantity and quality of letters of recommendations. 

I'll first give some background about my current application. I have a 3.0 cumulative GPA (there is a valid reason for a few low grades early on in my career which I won't get into here, but my GPA has increased dramatically since then), my physics GRE score is a little low and my general is above the 55th percentile in all three fields. 

I have two strong letters of recommendation. One from the director of my lab, and one from the head of experimental physics at my university. My question is regarding a third letter. Most applications state that 3 letters are required. I have two options for the third letter at this point; the first being from my advisor, who I've never taken a class with but knows me well, and the other is from a professor who said he'd write me one but it wouldn't be very strong as he can only discuss my character and, to quote him, "general interest in science".

I'm afraid that a third letter would hurt my application, regardless if two of the letters are strong. How damaging would two letters be in applying to a physics graduate program?

Thank you.
If the application calls for three letters of recommendation and you only submit two, your application may be considered incomplete and may not be considered at all.

So if you don't have a third letter, you're going to have a problem. But if the third letter is weak, it will hurt your application, too, which means you're stuck between a rock and a hard place.