Loud Thud Feeling When Braking

When I pump on the brakes coming to a stop, there is no THUD noise. I took off the cover to my master cylinder and saw that the rubber was fully expanded and the fluid was very low, almost to the bottom, could this be just from driving today?

The THUD noise happens noticeably when I first start the car from a cold start and when I stop for errands and then drive off, when I brake at a stop sign there is one, loud distinct BOOM.

I also checked my Automatic Transmission fluid and found it was a little low and there were bubbles on the dipstick. I put the car in park, I checked it on a sort of even surface, and refilled. When I drove off, there was a louder THUD when I was braking.

Holding the brakes down when coming to a stop is when it always happens. Is there any safety issue right now? I'm going to get it checked out but I dont want to drive it too much if it has the possibility of breaking. Thanks.