Clockwork Aquario is an action-platform game reminiscent of Super Mario Bros. and Wonder Boy III: Monster Lair, where players assume the role of Huck Rondo, Elle Moon or the robot Gush through five stages in order to stop Dr. Hangyo with his plan to take over the world.

[33] HobbyConsolas' Daniel Quesada praised the game's steampunk-esque design, Shinichi Sakamoto's soundtrack, dynamic co-op multiplayer and presentation but criticized its short length, unbalanced difficulty curve, repetitive and low quality character voices and overall visibility due to the colorful visuals.

Maciejewski found its pick-up-and-throw gameplay mechanic to be unconventional and gave positive remarks to the visuals, cartoon-style artwork, energetic music, frantic multiplayer and presentation.

[40] Nintendo Life's Kerry Brunskill gave positive commentary to the pixel art, creative stages and multiplayer, but noted its short length, certain aspects of the presentation and extra modes for being minor variations of the main game.

[1] Hardcore Gamer' Jeremy Peeples stated that "Clockwork Aquario is a fantastic action-platformer that blends quick-moving playable characters and enemies alongside an inventive attack strategy.

Peeples felt that the grab and throw mechanic was reminiscent of Treasure titles like Gunstar Heroes and Dynamite Headdy due to its depth and controls, while praising the addictive gameplay, accessible difficulty, audio design and visuals.

[34] Nintendo World Report's Neal Ronaghan commended the 2D sprite-based visuals and fun co-op multiplayer but criticized its short length, confusing menu interface and lack of additional content, regarding it "more as a curiosity than a game to keep coming back to.

"[37] TouchArcade' Shaun Musgrave criticized the title's short length, as well as superfluous ideas and mechanics, though he commended the stages' visual variety and found it to be a fascinating piece of history.

[39] Destructoid's Chris Moyse also reviewed the PS4 version, giving positive remarks to its visuals due to the sprite work and detailed backgrounds, whimsical soundtrack and 1990s anime-style aesthetic, but found the gameplay to be standard and noted its short length given the asking retail price.

[32] The Games Machine's Danilo Dellafrana praised the audiovisual presentation, artistic direction and smooth frame rate, but felt that it was "Perhaps too linear and simple for today's audience.