Shaggy and Scooby are asked by a mysterious swamp witch named Lila to find ingredients for her while helping their friends solve mysteries.
This game provides examples of the following tropes:
- Bigfoot, Sasquatch, and Yeti: The second mission features a giant yeti that turns out to be an animatronic disguise.
- Bubblegloop Swamp: As the name of the game implies. The initial hub area is the eponymous swamp, although it is not the main setting.
- Continuity Nod: During the second mission, Daphne mentions dealing with the Phantom the last time they met her cousin Anna, a callback to Episode 1 of First Frights.
- Creepy Cemetery: Not one, but two haunted cemeteries in El Muncho!
- El Spanish "-o": The second world is a Mexican-esque Western town named El Muncho.
- Final Boss: The final boss of the game is Lila's pet alligator Suji.
- Four-Legged Insect: Much like Scooby-Doo! First Frights, spiders only have 6 legs.
- Ghost Town: El Muncho, due to El Scaryachi scaring most of its inhabitants away.
- Giant Spider: Spiders appear in each of the three settings, though are quite rare. The largest of which is found in the swamp.
- Good All Along: Lila gives the impression of manipulating Scooby and Shaggy, but in the end it turns out that she just needed help making food for her pet crocodile Suji.
- Identical Twin ID Tag: The first mission has twins Emilio and Esteban. They wear clothing that mirror each other, plus Esteban has a blue belt while Emilio wears an orange belt in addition to having facial hair.
- Killer Teddy Bear: The evil teddy bears from First Frights reappear in the chalet attic.
- Laugh Track: Like its predecessor, Spooky Swamp has a laugh track in its cutscenes.
- Never Smile at a Crocodile: Played with. The game's final boss is Suji, the giant alligator, but after she is fed she is no longer a threat.
- Palette Swap: The arctic wolves have the same character models as the werewolves from the previous game, albeit colored white.
- Pet Monstrosity: Lila's pet giant alligator, Suji.
- Savage Wolves: The Arctic Wolves at Howling Peaks, which are palette swaps of the werewolves from First Frights … meaning they are aggressive and bipedal, unlike the actual animal.
- Shifting Sand Land: El Muncho, which is set in a desert Mexican-themed ghost town.
- Ski-Resort Episode: Howling Peaks is a popular tourist ski resort that has been abandoned due to the monster reports the gang are investigating.
- Slippy-Slidey Ice World: Howling Peaks, as mentioned above, set at a snowy ski resort, mountain and forest.
- Snowlems: Both the Snowmean and the Lurker enemies. While the Lurker can be descriped as anthropomorphic snow itself (it rises from the ground into a human-like figure), the Snowmean is modeled after a pretty generic snowman with stick arms, a carrot nose, and a hat - but, you know, mean.
- The Voice: Anna's boss Sergio is only heard speaking, being too cowardly to exit the basement door after Shaggy and Scooby run the errands he asks them to.
- Wide-Open Sandbox: Unlike its predecessor, First Frights, Spooky Swamp features three different open worlds that can be revisited after completing the game.
