The film sparked controversy after it received an 18+ rating from Brazil's Ministry of Justice for "explicit sex" and "drugs" - which restricts the film's audiences to people over 18 only. Some thought that the rating was not based solely on the film's contents and viewed it as a sabotage and foul play by the government against the film in an attempt to damage its commercial prospects in retaliation for the film's Cannes protest. On appeal, the film was re-rated to 16+.
Aquarius was again embroiled in controversy after critic Marcos Petrucelli, who was part of the special selection committee in charge of choosing Brazil's submission for the 2017's foreign-language Oscar race, made biased remarks on social media about director Kleber Mendonça Filho's politics - which was viewed as an attempt to keep the film from potentially representing the country at the ceremony. This resulted in an outrage where some resigned from the selection committee and directors withdrew their films from the submission process in protest to local politics interfering with the ability to fairly choose its candidate, such as Gabriel Mascaro (Neon Bull (2015)), Anna Muylaert (Don't Call Me Son (2016)) and Aly Muritiba (To My Beloved (2015)). Brazil's Ministry of Culture remained silent about the matter and shortly after, the still unseen Little Secret (2016) was officially announced as the country submission to the 2017 Oscars, chosen among 16 other candidates.
During the film's premiere at the Cannes Film Festival, the cast and crew the film staged a protest against the allegedly illegitimate impeachment of then Brazilian president Dilma Rousseff. They held signs reading "Brazil is experiencing a coup d'etat" and "54,501,118 votes set on fire!", a move which has generated both praise and calls for boycotts, a measure of the political division Brazil was experiencing.
Sonia Braga was the first and only choice for the role of Clara and director/writer Kleber Mendonça Filho has said in several interviews that the movie wouldn't be made if Braga wasn't part of it. Braga has said that she absolutely loved the script and it was the first time she was astounded by a screenplay to the point of almost doubting such a project would get made.
After the whole controversy revolving the film's selection as a possible nominee for the 2017's Oscars in the Best Foreign Language Film category, the North America distributor Vitagraph Films decided to release an independent campaign for the movie qualify for the major categories, with a focus on lead actress nomination for Sonia Braga. Although many news outlets were highly favorable of her performance, even naming Braga as a possible nominee, the film wasn't nominated in any category due to the fact that Vitagraph Films failed to file the proper paperwork to make the film up for an Oscar nomination.