I recently encountered this question while browsing the net and thought it was a important question for neti pot users. While I do not think there is an answer set in stone, my personal preference is to try to get water behind the nostril that is clogged. (That’s assuming both aren’t giving you problems).
I do tend to have more problems with my left nostril getting blocked at night while I sleep. The best method I have found is to flush the water through from the right side and try to get the debris and mucus to wash out the left nostril. In other words, I am getting the saline mixture behind the congestion and trying to wash it forward instead of trying to push it through the nasal cavities.
If you find that both nostrils are congested, then try to see which one allows you to exhale the most from and then flush from the other side. You may end up trying from both sides to obtain a good flow of saline.
Just to summarize…try to flush from the opposite side to see if that helps you get rid of congestion in a certain nostril.
