This episode provides examples of
- Animal Mecha: The giant mecha whale counts as Subtype 1
- Atlantis: briefly mentioned by Don and Mikey when they sight the underwater base. In addition, the name of the episode is a composite of 'junk' and 'Atlantis'
- Dead Hat Shot: Done with the nameless boat captain at the beginning.
- He's Back: The Garbageman
- Mugged for Disguise: Mikey and Don do this to a couple of mooks
- Sarcasm Mode: When Splinter is splashed by river water he says "Just what I needed; another bath"
- Shout-Out: Mikey asks Don "Aren't you a little short for a junk trooper?". Later he also says "To the Shell Sub, Boy Wonder"
- Underwater Base: The Garbageman's new base of operations