- In the premiere, the camera does a 360 spin as Riko runs toward the viewer, echoing a similar shot with Honoka from the first episode of the original series. This specific camera angle is reused during the first episode of Season 2 as a Call-Back, as well as in "Bokura no Hashittekita Michi wa..." in The Movie.
- Chika mispronouncing µ's as "yooz" initially, which is also how Honoka also mispronounced it at first. In the English dub, Chika mispronounces it as "mousse", just like Honoka.
- Just like Honoka's "ほ" and "Ho." sweaters, Chika has "チ" and "Mikan." sweaters.
- In Season 1 Episode 3, Yoshiko appears wearing a mask and sunglasses, as to conceal her identity, just like Nico Yazawa.
- In the opening scene, You is doing something similar to Kotori's signature photobomb.
- For a meta nod to the first series, the ADR director of the dub is Maki's voice actor, Caitlin Glass.
- The training schedule Dia used in Episode 10 is the exact same one Umi drew up in Episode 10 of the first series, just with an "Aqours" label stuck over "µ's".
- At the very end of Episode 12, Chika suddenly sees a feather slowly falling from the sky, grabs it while looking rather stunned and then smiles as she holds it; this final shot is extremely similar to Love Live's second season ED, where several feathers fell from the sky and each episode had a different girl grabbing one of them and smiling at the camera.
- Season 2 as a whole tends to reference other canons and supplementary material much more than Season 1, such as showing Mari's taste in Industrial Metal and pointing out Hanamaru's dislike of noodles. Ruby is also mentioned to have designed the outfits worn for "MY Mai TONIGHT", a character trait from Dengeki canon that was originally thought to have been discarded since You typically fills the position of costume designer in the anime.
- The latter half of Season 2, Episode 4 is one big reference to the "Koi ni Naritai AQUARIUM" PV, as it features Aqours working part-time at the Izu-Mito Sea Paradise, complete with similar outfits. You even dresses as Uchicchii, as in the PV.
- In Season 2 Episode 5, Riko's drawing of Anko resembles a real drawing of a dog Rikyako sketched in an interview.
- In Season 2 Episode 7, You and the rest of Aqours perform an animated version of Shuka Saito's call and response used in live Aqours concerts.
- In the "Welcoming Sarah and Leah with Hospitality!" audio drama, Ruby is dressed in a coelacanth costume, poking fun at the infamous April Fools' Day puppet show.
- The subunit versions of "Hop! Step! Wai!" feature the subunit performing their subunit stage introduction in the middle of the song, capped off with the subunit shouting "Hop! Step! Wai!" at the end.
- A series of special nesoberi keychains released for Comiket 94 feature all of the Aqours nesos with sleeping faces except Mari, who is wearing the anime eyepatches from Season 1 Episode 10.
- The opening song of Over the Rainbow, "Bokura no Hashittekita Michi wa...", contains a few nods, especially to "WONDERFUL STORIES", which canonically precedes it.
- The very start of the song starts with Aqours standing in the same positions as they were during Chika's solo in "WONDERFUL STORIES". The stage in the background also reuses the same setpiece.
- The instrumental portion contains shots of various members dancing in front of a variety of locations. These include the shop that Yoshiko is working at in the "HAPPY PARTY TRAIN" PV and the observation deck where Mari confronts You in Season 1.
- The same curtains that ended the anime are seen opening up at the end of the song.
- The MV for "Dazzling White Town" features locales in Hakodate that were seen in the anime, such as the cafe that Sarah and Leah run and the street where "Awaken the Power" was performed.
- "PURE PHRASE" prominently shows Riko wearing her "Omoi no Hitotsu ni Nare" outfit with the scrunchie on her wrist. She is also accompanied by her pet pug that she adopted in the series finale.
- Ruby's second solo MV, "Cotton Candy Ei Ei Oh!", references a few scenes from Season 1, such as the Little Demon No. 4 promo video and the scene where Yoshiko locks her in a grappling hold. There's also a shot of multiple Rubys appearing on screen towards the end of the video, some of them with outfits that she has worn over the course of the series.
- Hanamaru's second solo MV, "Akogare Ranraran", references several scenes with Hanamaru from the anime and the movie.
- Mari's second solo MV, "Shiny Racers", is one big shout-out to Season 2 Episode 10, with Mari driving her Volkswagen Type-II van and singing in her car as it barrels down the road. The van also flies into the air in front of the full moon, just like in the episode. The music video ends on a redrawn scene from this exact episode in the anime where Mari pulls up in her van in front of the Tochiman Inn, revealing the entire music video was Mari's Daydream Surprise.
- Unlike the other solo album covers, which are mostly original artwork and costumes, Yoshiko's "In this unstable world" solo album cover is one big love letter to Aika Kobayashi's performance of the song during Aqours 2nd live. The cover features Yoshiko sitting on a throne much like how Aika did during the song, and the costume replicates numerous features of the costume that Aika wore for the performance, down to the matching hairstyle.
- Two of the pixel art scenes in "Tatehoko Tsubasa" reference the first episode of the anime where Yoshiko falls out of a cherry tree and runs away. She is also seen sleeping with a plush shark similar to the shark hammock she used in Season 1 Episode 10, and the "shmup" scenes in the video show her destroying mikans, alluding to her aversion to them.
DREAMY COLOR PV
The "DREAMY COLOR" PV, the first proper live-action PV in the franchise, is full of references to the anime that it deserves its own section.
- The order of the solos is a reference to the order of the members joining in the anime: Chika first, then You, Riko, Ruby, Hanamaru, Yoshiko and finally, Kanan, Mari and Dia.
- The blue feather is a reference to the blue feathers in Season 2, a symbol of Aqours' radiance.
- Anchan and Shukashu, who voices Chika and You respectively, are filmed at the rooftop of Nagaisaki Junior High School, the real life basis for Uranohoshi. The rooftop serves as practice grounds for Aqours in the anime.
- Rikyako is filmed in the school's music room. Riko plays the piano here in several episodes.
- Furirin and Kinchan, who plays Ruby and Hanamaru respectively, are in the school's library. Hanamaru joins Aqours after being encouraged by Ruby in their school's library.
- Aikyan is filmed in the cherry trees near the school where Yoshiko fell down in Episode 1.
- Suwawa is filmed near the Frog House and in the Awashima Shrine steps in Awashima Island. Kanan lives in Awashima Island, her house is based on the Frog House and she jogs to Awashima Shrine as part of her daily run.
- Ainya is filmed in one of the school's hallway. The same hallway is seen in the anime and is where Mari confronts Dia about running away.
- Arisha is seen writing "Aqours" on the beach as a reference to Dia writing "Aqours" on the beach in Season 1 Episode 9. She is also seen at Tougou Beach for her solo, where the scene took place.
- Ainya, who voices Mari, is seen in the music room of Awashima Hotel. Mari's mother plays the piano here in The Movie.
- Suwawa, Ainya and Arisha have scenes near the fountain of Awashima Hotel. The same fountain is of great importance to the third years, being the place where they first met.
- Anchan is seen in the corresponding room where the School Idol Club room should be.
- The gymnasium in the first chorus is the same gymnasium where Chika, You and Riko performed "Daisuki Dattara Daijoubu!".
- The Tokai bus, a local bus company, makes an appearance in this PV and in the anime. The scene inside the bus is a reference to "Yuuki wa Doko ni? Kimi no Mune ni!" which has the girls inside the bus. The close up of the stop button is a reference to their first PV, "Kimi no Kokoro wa Kagayaiteru kai?", which has a similar scene.
- The floating lanterns near the end is a reference to "Yume de Yozora o Terashitai" in the anime, while the fireworks display is a reference to "Mijuku DREAMER".
- The voice actresses jumping during the sunset is reenacted from a similar shot in "Aozora Jumping Heart".
