No, it does not affect your brain but it may harm your nasal tissues or cause an infection in your mid-ears if your nose is blocked. Many patients develop ear infections due to improper use of sinus rinse. Particularly, neti pot is very risky for people whose noses are blocked. This is something I want to warn people against. Please read further from here: http://www.HowToGetRidofSinusitis.com/nasal-irrigation
. It teaches the safe ways.