- Angst? What Angst?: The usual Trapped in Another World kind with Jason, who's remarkably quick to adjust. Then again, only one person went to see him off on a potentially deadly mission, so his connection to home doesn't seem to be that strong. This trope is also justified as Jason actually is from Atlantis, making 'our' world the one he was trapped in.
- Big-Lipped Alligator Moment: Possibly the first time that a story has actually started with one. Jason is from the future, and his adventure begins when he takes a submarine down to the bottom of the ocean — yet once he wakes up in Atlantis this is never brought up. There's no Fish out of Temporal Water storyline, he just adapts to his new surroundings instantly and never mentions his past.
- Ho Yay: Plenty of it between Pythagoras and Hercules. They are Heterosexual Life-Partners who argue Like an Old Married Couple and when facing certain death all they can do is tell each other that It Has Been an Honor and hug.
- Not to mention Jason and Pythagoras, which already has a good following on the internet. The Jagoras shippers will state the significant looks between Jason and Pythagoras, the luminescent blush Jason sports once while looking at Pythagoras, the fact Jason switched places with Pythagoras to stop him being sent as a tribute to the Minotaur, then Pythagoras was so quick to offer to go on a life-risking mission to rescue Jason from being killed as a tribute to the Minotaur, the rather...cuddly first meeting, the walking extremely close to each other, and Pythagoras constantly checking an oft-topless Jason out. Blatantly. Fans reckon its only a matter of time before it becomes canon.
- In the season 2 premiere, Pythagoras outright says "I love you." to Jason and Hercules, without really elaborating on whether he means platonic or romantic love. To add to that, he mentions he really doesn't understand his feelings, meaning it's possible even he doesn't know.
- Retroactive Recognition: Anya Taylor-Joy as Cassandra.
- The Woobie: Medusa, after being turned into a Gorgon.
- Tear Jerker:
- When Pasiphae sentences Ariadne to be executed in the finale, a terrified Ariadne looks to her people for help. Not one person steps up to defend her from the queen.
- Orpheus killing Eurydice, then swearing to look for her in the afterlife. We all know how that turns out.
- When Hercules bursts into tears when he finds out about Medusa's sacrifice is quite hard to watch.
YMMV / Atlantis