James Gunn confirmed that The Suicide Squad can largely be considered canon within the new DC Universe, with no fundamental obstacles. However, some timeline details still need to be handled flexibly to align with existing continuity.
On the official Spotify podcast "The Suicide Squad: Is It Canon?", Gunn discussed the film's timeline relative to the new Superman movie. The fact that Bloodsport shot Superman with a kryptonite bullet does not necessarily mean Superman was defeated in battle; however, given that Superman has only been publicly active for three years in the new setting, the film's events may need to be adjusted to 2023 or 2024.
Harley Quinn also raises continuity questions. Gunn is unsure whether Margot Robbie is willing to continue playing the role, as she has no contractual obligation. Since the Joker has not yet been established in the new DC Universe, there is room to reinterpret whether the ex-boyfriend Harley mentions in the film is indeed the Joker.
Other characters have already taken different paths. Weasel has returned in Creature Commandos, and King Shark may appear in the show's second season. Gunn also likes TDK and Ratcatcher 2, but since Nathan Fillion is already playing Green Lantern Guy Gardner, TDK would likely be recast if he reappears. Gunn also admitted that building a connected universe inevitably leads to some inconsistencies.