- Episode 5: Little Marie tells Nadia and Jean about how her parents were shot by Gargoyle's soldiers, ending her recollection in tears. Later, Nadia and Jean dig graves for Marie's parents, and tearfully reveal to the little girl that she'll never see her mother, father, or pet dog again. The episode ends with all three weeping at the graves, with Marie lamenting, "I want to go to Mama and Papa!"
- Episode 15: The climax of this episode involves a genial sailor, Ensign Fait, sacrificing his life to save the Nautilus both from a lethal gas leak and from being captured by the American battleships. What makes this moment truly heartwrenching is how Jean gradually becomes crushed when he vainly argues for the sailor to be rescued. Fait's death scene, incidentally, is truly terrifying, in which the sailor coughs uncontrollably to his death after screaming "Oh no! I don't wanna die! There's so many more things I wanted to do!" right after he told Jean that it was okay because he lived a good life. To have him completely contradict that right after, and in such a desperate manner, made this a huge Tearjerker. Jean's breakdown is similarly heartbreaking: he pounds his fist hopelessly on the sealed hatch to the engine bunker, calling Fait's name until he finally collapses on the floor, wailing hysterically.
- Episode 16: The entire episode involves a trip to the Atlantis graveyard, in which the heroic sailors are laid to rest. Here, Jean discovers that his father has been killed by Gargoyle. As if he hadn't already been heartbroken, he becomes extremely depressed and even considers giving up inventing. Then, in a Heartwarming Moment, Nadia, genuinely worried about Jean, comes by and tries to comfort him; the episode ends with her weeping on his shoulder while they stand beside the funeral.
- Episode 22: Electra's entire flashback scene. And the ending of that episode.
- Episode 35: Nadia tearfully reveals that she feels like a totally selfish, unloveable person and tries to commit suicide to escape from her fate. Instead, she is gently lowered to the ground by her Blue Water ala Sheeta's crystal in Castle in the Sky (although this is revealed, not seen). Her friends are all traumatized by what she has done (Grandis slaps Nadia across the face, while Sanson calls her out for "playing this tragic little game of yours!"), but Jean kindly tells Nadia that he doesn't care about who she thinks she is, or even about her origins as an Atlantean—he loves her anyway. Nadia is so moved that she tearfully apologizes (perhaps also for other unkind words/things she said/did to him too). Later, they discover that it's Nadia's birthday and have a wonderful celebration.
- In that episode, Nadia's breakdown after she explained what she's afraid she'll end up doing with Blue Water has her verbally deconstruct herself in a way that's pretty hard to listen to.Grandis: You must believe in yourself! So you can escape this fate!Nadia: What is there inside me that I can believe in myself, Grandis?! Im selfish, and mean, and always get the people I love into trouble! Ive always been a frightened little girl! Always running away! When I finally had the chance, I didnt say goodbye to the man I knew was my father! I hate myself! Truly hate myself! Theres nothing good in me! Im just a spoiled girl whos inherited the awful power of Atlantis!
- In that episode, Nadia's breakdown after she explained what she's afraid she'll end up doing with Blue Water has her verbally deconstruct herself in a way that's pretty hard to listen to.
- Episode 38: The Grandis Gang sacrificing the Gratan in order to cripple Red Noah to turn the tide of battle. The tank's been a part of the show since the very beginning and it's arguably just as much of a character as the Gang at this point. So it's destruction is a punch in the gut — and demonstrates that with the series in its final battle, anyone or anything can die.
- There's also something simultaneously heartwarming and heartbreaking in that while the Gang's decision to sacrifice the Gratan is unanimous, it's ultimately Hanson who detonates its self-destruct charges. He designed the tank and now he has to kill his own mechanical baby to save their friends aboard the Nautilus. Hanson tries to be stoic like Sanson before pulling the trigger...but he's still clearly heartbroken.
- Episode 39. All of it.
Tear Jerker / Nadia: The Secret of Blue Water