I'm having a hard time trying to decide which master degree i should choose. I love both fields in a way i can't even explain, even though they are not highly related. I've been thinking about getting both degrees but i'm not sure how that will affect my carrier, since i wanna persuit an academic one. What should i do? Any thoughts?

Think one more step further.

For example, Prof Frank Wilczek had a master degree on Mathematics, and a PhD on Physics.
It also depends on whether you are going pursue master degree in UK or US etc...

I take it your background (undergrad) is Civil Engineering. Both fields (civil & physics) are quite diverse, you would do well to elaborate what key fields you are keen to go in. You may also be aware that admission to either of the above would require meeting certain prerequisites. Under civil engineering we have structural, hydrology/water, environmental, construction, geotechnical, etc. Physics can also have various specializations like nuclear, quantum, medical, plasma, to mention but a few. If your undergraduate was in civil with a bias towards structural, it'll be extremely difficult to be admitted into MSc Physics specializing in medical physics.