Okay. Let’s talk about this for a second.
Haru accepts Rei into the team. Rei is, at this point, still rather new and doesn’t share the close bond the others all have with each other. Haru letting anyone new into his life is rare, he doesn’t want anyone getting too close (except Makoto obviously.). This is apparent when Rin first shows up in their childhood, he’s hesitant and suspicious about allowing this stranger in (of course he does eventually).
So this new person he let in, was almost responsible for killing Makoto, the one constant person in his life. (His parents left, Nagisa went to a different school, Rin went abroad, his grandma died.) You can see it in his expression and his eyes, he’s fricken pissed at Rei. Rei made him come to the realization that Makoto wouldn’t always be there, Makoto wasn’t invincible. Made him confront some feelings he wasn’t ready for. This new person hurt Makoto.
Makoto may not hold it against Rei because of his personality, but Haru does. If something had happened to Makoto, I can almost bet Haru—in a grief stricken state—would physically lash out at Rei before retreating into the darkness of his mind.
But then Nagisa tells Haru why Rei was swimming and his expression softens, it’s almost like he felt bad for getting angry at Rei. Rei was just trying to be a better teammate, he was just trying to be the best he could be for them, and then Nagisa points out the blame is also on Makoto for attempting the rescue alone and Haru for going in without help (although he did join him quickly so he’s also to ‘blame’ so to speak). Haru, while probably still slightly annoyed that he had to face terrifying aspects of life thanks to newcomer Rei, decides to protect Makoto the rest of the episode. This is especially clear when Rei tries to push for Makoto’s back story, Haru snaps at him and I can almost imagine in his head going “Shut the fuck up man, you’ve caused enough emotional trauma for one day.”
I have no idea what point I was trying to make, but I like discussing things about Free! okay?