Such a great question. At any school, big or small, D1 to D3, the athletes are going to be spending a lot of time on their sport and with their teammates in a way that cannot be anything but exclusive of non-teammates. At big (D1) schools, for example, students often talk of wanting to meet players, who may be celebrities of sorts! At D3 schools, they are more accessible but yes, also segregated for part of the time.
Practices, games, spring training, service obligations, etc. are all things that separate them from others and help them bond with each other. And because the rhythm of their lives may be different – rowers who need to be on the water at daybreak, for example, or athletes that don’t party during the season - it’s also often attractive for them to room together because they too feel some isolation from the rest of the student body.
With all that said, my sense (having been a D3 athlete back in the day and having also been the parent of one), the smaller schools offer a better opportunity for athletes and non-athletes to mix, and I think that desire is genuine on both sides to do so. Some of it is at the beginning, like orientation trips. Some is during the school year - short terms in particular - but also smaller classes, study groups, even housing arrangements that allow and encourage regular interaction. Study abroad - even short term travel - opens up new social avenues. And kids this age are often looking for that!
For a kid who has always done sports, I think there is a bit of a feeling of missing out - especially at the beginning while new freshmen are looking for their people. - But the athletes likewise complain of not being able to do outdoor club snowshoeing weekends or hikes, and more than a few will abandon their sports to have the freedom non-athletes had from the get-go. It helps to have non-athletic interests as athletes and non-athletes alike will host radio shows, sing a capella, do volunteer work, etc. And at some of these schools, everyone attends hockey games or whatever.
I would suggest you ask students less about the divide and more about what structures exist to facilitate mixing. Orientation. Campus wide traditions. Departmental events. Short terms. Housing. Intramurals. Definitely ask about weekends, what people do, and who is doing the arranging.
The tldr answer is yes, there is some segregation, especially early on, and also, given the smaller campus and desire there new people and socialize, it’s often a non-existent line by graduation.