In the first episode of the anime, Mugi is making a big deal out of mixing her fries with those of the other two girls. In Japanese culture, sharing your food with the group is a sign that you accept the group as your own, so Mugi was both being formal and very sweet in one go.
The train station seen most in the series, which is the one Mugi uses for commuting, is the Shugakuin Station on the Eizan Electric Railway in Kyoto.
The high school is based on an elementary school in Toyosato in the Shiga prefecture. The building was supposed to be torn down, but after protests from the local community it got renovated and opened for the public, and it now serves as a museum. It's needless to say that the building is now a very popular destination for fans of the series.
The Max Burger fast food restaurant frequented by the girls is based on a real-life McDonald's.
In episode 5 of the first season, Sawako plays her super flashy solo. However, the way she moves her arm while "speed picking" is something more akin to new guitar players. Faster playing is done using mostly the fingers or the wrist, Sawako's using her arm almost exclusively.
The place where the girls go to feed the Japanese monkeys, as seen in in episode 4 of the second season, is the Iwatayama Monkey Park in Kyoto, situated on top of Mt. Arashiyama. It is pretty much as depicted, including the splendid view of the city.
The statue seen at the very end of episode 7 of the second season is based on a statue of◊ William S. Clark, the founder of Sapporo Agricultural College (now Hokkaido University), which implies that Sokabe-sempai is studying in Sapporo. Also, the full version of "Cagayake!GIRLS" contains the words "Girls, be ambitious", which is a reference to Clark's famous parting words to his students ("Boys, be ambitious!").
Ton-chan is a pig-nosed turtle, a species that is actually hard to keep in captivity, since it's rather aggressive and prone to stress and illnesses. It takes dedication and specialized knowledge to care for one, so one wonders whether the girls would be up to the task. It might be especially unwise to keep it in a place with lots of noise, like where a band is playing.
The festival the girls and Sawako attend in episode 12 of the second season is based on the Fuji Rock Festival, which is held annually in the Naeba Ski Resort, in the Niigata Prefecture of Japan.