Salacia - Manga
Summary
In 2071, north pole ice have melted and the land has been submerged. Humanity survived but it's divided into two species: the true humans, those who live in underwater cities, and the Dugons, those who chose to undergo genetic modification to live in the sea. Both species go to war to survive as long as the Dugons consider the humans good to eat. To defend against the Dugons, the city of Mari Ramelle builds a new kind of weapon, the mermaid robot, Salacia. Because of the small size of the the pilot cabin, the robot is piloted by a girl and a boy, both 13 years old: Marin Yuuki and Ushio Mizushiro. The fight for survival is hard, and during the manga, the city builds more mermaid robots.
... and the second season of the Anime did a better job of pacing than I thought they would. I think they moved the Elf village arc from before hostilities with the Principality began to the inter-war period, aka the start of the second season, and used that to pad it out. Good call if that's what they did. In any event. Good season.