All I can remember was, a Ninja Club (in University, I think) was about to be removed since it had no members and I think the protagonist was forced to join.... and (might be wrong) the club owner has connections (is an uncle i think) to a girl that the prot agonist likes (I think)
One scene was where he was traning underwater with a straw ... and all the members left because it was a harsh training

I might edit or post reply if I remember more.

Sorry that the description is messy and insufficient.

I don't remember the scene with underwater training but, maybe Karate Shoukoushi Kohinata Minoru? Something similar happens: ninja club with only one member (the brother of the protagonist's love interest), college setting, protagonist forced to join for a while.

I just checked that one, I don't think its that manga. Tnx though