— Makoto, speaking to Haruka
Makoto has known Haruka for his entire life, having met when they were just months old, and is his best friend. As a consequence of being together for so long, Makoto is able to read Haruka's mind, understands Haruka's good points, and is often forced to speak as his spokesman. When Haruka doesn’t want to speak anymore, he just "leaves it up" to Makoto to speak for him. It allows Haruka to act aloof and stoic, but still get his thoughts across - though they aren’t stated to be his, necessarily.
He is extremely used to having Makoto always there to help him with making decisions and even speaking up his mind, and when he feels like Makoto oversteps his boundaries, he dismisses him in his mind as a meddlesome guy. But secretly he really appreciates his efforts.
Both have had near-drowning experiences; In the sixth grade, Haruka fell into a river and was saved by Makoto and Rin. During the training camp on the deserted island, Haruka saves Makoto after he fails to save Rei. When Haruka brings Makoto to shore he is terrified when he realizes Makoto is unconscious, and is about to perform CPR, but then Makoto coughs up water and regains consciousness. He tries to sit up and look for Rei, but Haruka tells him that he should be resting and holds him down. Shortly afterwards, Makoto tells Haruka that he is the biggest reason he still swims and gets close to the ocean because Haruka does, and he cares that much for Haruka and what Haruka loves, enough to put his fear aside so he can enjoy it with him, wanting to share the experience, to understand what makes Haruka the happiest, and so he overcomes his fear for it. Makoto wants to understand and feel the same emotion as someone else to the point of conquering a deeprooted fear — something that gave him a panic attack, made him stop moving in the ocean during a storm, while trying to save someone, despite himself. Haruka then gasps, showing that he himself didn’t even realize what he was to Makoto until Makoto told him so.
Makoto and Haruka are often seen doing things together, such as sharing rooms, going to school, and having lunch. They live very close to each other with Makoto's house being visible from Haruka's. Specifically, Makoto's house is at the bottom of the stone stairs leading to the shrine near their house, with Haruka's house being up the stone stairs, just past the first torii gates. It is not uncommon for Haruka and Makoto to wait for each other on the stone stairs.
They are very close and care for each other greatly. In the beginning of the series, Haruka didn't express himself as much, although Makoto always knew what he was thinking. Throughout the show, Haruka begins to speak his mind more often. 
It is shown that Haruka bought Makoto four aquarium fish. Nagisa told Makoto to name them Nagisa, Rei, Haruka and Makoto, however Haruka told him that it's better to name them Mackerel, Bonito, Tuna and Jackfish.
As Makoto and Haruka become third-years, both of them have to think about their futures. Makoto becomes worried for is friend, seeing that Haru starts losing his way in finding what he's going to do in the future. Makoto is unsure of what to write on his career path questionnaire while Haruka simply writes "Free", showing he doesn't care about getting a job or continuing schooling. When Makoto asked him about his future plans, he said that "as long as he can swim, he doesn't care", leaving Makoto smiling and commenting how that sounds just like him.
Nagisa and Makoto are close friends, despite having not been in contact for a few years. While both are generally outgoing and positive, Nagisa is bouncy and Makoto is kind and sensitive. They care for each other. Makoto also knows when something is up, for example at the squid festival when Nagisa was acting paranoid and gave Makoto a wink, he knew to wait for a moment without Haruka to ask Nagisa what was going on.
Makoto and Rei have a good senpai-kohai relationship. Makoto tends to act towards Rei as an older brother and often draws him away from Nagisa's constant hyperactive activities.
Makoto was ready to risk his life in order to save Rei from the storm.
Makoto and Gou have a good, friendly relationship. Makoto was the first one to notice Gou and the first one to actually realize that Gou is Rin's younger sister. Since the day Makoto and Nagisa ran into Gou in front of Haruka's house, all three of them started hanging out a lot and spending time together at school. After having a talk with Makoto at the school pool, Gou decided to join Iwatobi High School's Swim Club.
Unlike in Gou and Nagisa's relationship, Gou never gets angry with Makoto, despite him calling her "Gou-chan".
It is unknown if Chigusa and Makoto knew each other before the squid festival, however, they are pretty friendly towards each other.
During the squid festival, Makoto complimented Chigusa and Gou for their looks, but Chigusa misunderstood him, thinking that he complimented their yukatas instead of their looks, making Makoto feel a bit uneasy.
Miho is Makoto's Classic Literature teacher as well as his homeroom teacher. He met her at the opening ceremony and could tell a lot about her to Haruka the next day. She had helped him and Nagisa when they were scolded by another teacher and later, she became a supervisor of the swimming club at Iwatobi High. Miho got angry with Makoto and Nagisa several times, usually when Nagisa wanted to make her wear a swimsuit in order to get more students to join the swim club. However, she would not be angry with him for too long, usually forgiving him right away.
In the High☆Speed! novel, their relationship is detailed a little further, impacted by an incident by the riverbank, where they save Haruka as their friend Aki rushes to call the ambulance and several contacts. After Haruka is hospitalized, Rin and Makoto walk to the bus stop together, with Rin expressing anxiety. Makoto tries to reassure Rin that Haruka will be fine, smiling--but Rin reveals the person he was scared for was Makoto, who, when they saved Haruka, couldn't stop shaking.
Afterwards, Makoto feels a responsibility placed on him by Rin to ask if Haruka would join the relay with them, and once they do, Rin and his relationship continues to build. From the riverbank incident on, Rin keeps a subtle eye on Makoto, at one point jumping in to calm him when he seems to have trouble with the water, and Makoto comes to find it easy to joke around with and tease him, and freely laughs at others' joking about him. As seen in the beginning of Free!, late in High☆Speed! Makoto realizes and becomes apprehensive over whether Rin will stay in Iwatobi or go some place else, and determinedly calls Rin by his first name--the second to last to do so--cementing their bond during these years.
When Rin returns to Japan from Australia, he ignores Makoto and Nagisa in favor of challenging Haru, brushing them off with "You're still hanging out with these guys Haru?" Makoto, still remembering their childhood bond, converses with Coach Sasabe worrying over why Rin had become so distant, and calls him afterward asking that he join Samezuka's swim club so that they could see each other some day soon. When Nagisa confirms Rin joined, he's very happy. And sometime later, despite Rin's supposed dismissal of him, when Gou mentions to Rin that Makoto came with them to the ocean, a flash of anxiety for him passes by his face again, showing that he too remembers their bond after all. He wakes up in the middle of a storm worried about Makoto, and in the morning runs to the beach to check if he and the team are safe.
It's only after Rin wins against Haru at regionals that the Iwatobi boys meet him again, bumping into him while looking for Haru. When Rin assumes Haru is upset due to losing against him, Makoto chides him, reminding him that swimming meant something more to Haru, and he's pretty sure that Rin was the one who taught him what it was. In the finale, after Haru and Rin heal their rift, Rin rekindles his friendship with the boys, able to laugh with them again.
In High Speed!, Aki and Makoto are amicable towards each other, with the latter affectionately calling Aki "Zaki-chan," much like he would later call Rin's sister and Iwatobi's manager "Gou-chan." Aki turns to him to understand Haruka more than she does, and Makoto is supportive of her a friend, such as when she loses her scarf, and when she forwards the idea of planting flowers around a lonesome cherry blossom tree.
Late in High Speed! they share excitement over each other's medley team doing well, culminating in a high five between the two of them.
Goro and Makoto have a good relationship. Goro used to be Makoto's coach while he was still a coach at Iwatobi Swim Club. One night, wanting to visit the abandoned swim club building, Makoto ran into Goro, but didn't recognize him. After having a talk with him (not knowing it was actually Goro), he recognized him as Coach Sasabe and told him that he was one of his students. Goro then noted that Makoto grew big.
Ren, Ran and Makoto have a good sibling relationship with one another as Makoto looks out for them like a big brother should.
- Main article: Ms. Tamura
Makoto and Mrs Tamura are neighbours and they seem to have good relationship. Ms. Tamura often gives Makoto food to bring with him when he passes by her house in order to get to Haruka's.