Most of the episodes involve the characters having done regular tasks around the ocean with each other. A lot of the characters appear in this spin-off, though a few may appear in the main series, other series, etc. If a character from another spinoff can handle water (i.e. Fiji, Tide), then they may appear sometimes.
There was a bit of a time frame when MMB The Coolest quit and he handed the series over to The Flying Pie. He took it back because TFP is inactive, but MMB made it so anyone can contribute to the series.
Many of the characters are fish or aquatic species, though some are mutants. One of the characters is also apparently a human in a diving suit.
- Angie is an anglerfish. She is very social and loves being around others, but she doesn't have very many friends due to her appearance.
- Annie is an anemone, who does not move at all, yet protects her best friend, Laughy.
- Betty and Benny are betta fish who are conjoined. Benny loves to fight to try to impress female characters (like Disco Bear-sues), but he doesn't realize that his girlfriend is part of him. Benny's deaths mostly involve getting separated from Betty, leaving Betty to get hurt and also die.
- Blasst is a sea bass with a motorcycle helmet who is a bit of a daredevil. He doesn't focus on his stunts, which often kills him. His name is a pun, not a typo.
- Blobert is a grey-pink blobfish who is noticeably shorter and fatter than other characters. He is almost always seen with an unhappy face. He is sensitive about his weight and appearance, as well as thinking he could be the only blobfish around, since he couldn't find any others.
- Bubblewrap is a cat-fish hybrid who is one of the antagonists in the series. He can live on both the land and the sea. He eats the main characters as a snack.
- Caviar is an egg that first appears in Season 2, is found in a hole around a shell. He unfortunately gets lost, and for the middle part of the series, gets protected by another character. They have to protect the egg from Koby, Quacks, and fishermen, however.
- Chopper is a multi-colored mantis shrimp who is an expert of kung fu. Like real members of his species, his strikes are as powerful as bullets. His complex eyes allow him to see in various directions, making it difficult to sneak attack him.
- Chuckly is a navy blue dolphin who likes to laugh whenever a joke or pun is heard.
- Chum and Chubbs are a duo of crabs. Chum is purple, while Chubbs is yellow. They have the body shape of Crabby. They occasionally come to the reef to comment on whatever is going on. Instead of gibberish or bubbling, they just talk in clicking, with captions. This means they don't speak English. Some CRFs, like Claw and Doppel, can speak their language.
- Claw is a pink crab. She loves to pinch things that feel tense. This is why she massages very badly.
- Cuttles is a cuttlefish who is enjoys time with friends but is somewhat rebellious and vain. He is able to change color to blend in with his surroundings.
- Delicious is a peach tuna who is a Giggles sue.
- Dignify is a butterfly fish who is very Smart, and is constantly attacked by oysters.
- Dipher is a seahorse who is very dumb. He is dating Delicious, and his pregnancy is due to the fact that father seahorses can get pregnant.
- Dooty is a baby cod whose parents apparently died when a coral tree crushed them. He has picked up on a lot of violent video games and rage talking on others' houses.
- Doppel is a robot designed to look like a fish.
- Goodevil is a yin-yang colored angelfish who is very kind, yet not so kind.
- Flotsam and Jetsam are duo characters. Flotsam is a friendly periwinkle otter while Jetsam is a fat leopard seal who eats all kinds of marine animals.
- Haggle is a hagfish who is a very skittish and fearful character in the series. She lives secluded at the bottom of the sea, hiding from predators and other deadly sea creatures. She often secretes slime if scared.
- Hingy is a clam which is a Splendid sue. He loves to save other CRF's.
- Hover is a dolphin who loves to help but ends up making everything worse.
- Insider is a ghost shrimp with visible body systems. Many young fish come to him when they want to learn about the digestive system. He is also really gross.
- Jammer is a purple jellyfish who likes to play guitar. He is bad however.
- Knick and Knack are twin mermaid bears with matching hairdo's of different hair colors, who are very friendly, but look very different from the other Reef Friends. They end up being ridiculed for this reason.
- Laughy is a clownfish who is a class clown. He loves to joke around, often getting into trouble
- Mackey is a normal colored mackerel with several halos made of some six-pack soda can rings held by a few pieces of fish pellets, and a toga who the reef friends come to when they need help, because of the phrase "Holy Mackerel" coming to the reef by an unknown source.
- Mate is a red marlin who is a Lumpy sue and a Russell sue. He is dressed like a pirate, is dumb, and has Lumpy's body shape.
- Mush is a seapig who is shown to lead an army of seapigs.
- Nighty is a sea star who is blue with yellow bumps. He is lazy and doesn't mind damage. He has a unique body shape compared to everyone else.
- Oily is a gray squid who loves to squirt ink at other characters, blocking them. His deaths mostly involve squirting himself and crashing.
- Overbite is a hammerhead shark, who like his name says, has an overbite. He often tries braces, but eats them. He is disliked by fish with good teeth.
- Puffer is a blowfish who puffs up when nervous, often leading to deaths.
- Quacks is the primary antagonist of the series. he cannot swim because of his nub. At his home, he has poached many coral reef friends, typically Generic Reef Friends.
- Ray is a manta-ray, who is a Handy-Sue. He has bandaged fins, yet can swim. He has difficulty lifting and grabbing things due to his fins.
- Shocker is an eel, who is a bully. He loves to shock fish for no reason.
- Slice is a sawfish who is similar to Lash because he has eyelashes.
- Sparkle is a goldfish, who is very greedy. He often gets jealous when he sees a tree friend with something he wants.
- Splashy is a diverman who is often hunting gold. He lives in the land, unlike most main characters. His appearance is unknown as he is only seen in his suit.
- Spongy is a sea sponge who can quickly regenerate lost body parts. He can also attach himself to objects, including other characters.
- Sucker Is a red octopus, who is concerned about safety. He doesn't follow his own rules. he has the highest survival rate out of all the characters.
- Surge is a surgeonfish who is a doctor.
- Teary is a shark with Lumpy's body shape, is smart, and is a Flippy-sue. He flips out when he is reminded of the War of the Sharks.
- Urgent is a sea urchin who always tries to do everything done, or something bad will happen.
- Wriggles is a nerdy eel who is Shocker's cousin. She keeps a freeze-dried worm in her lunchbox in case she gets hungry, but she loses it a lot.
Not for Profit
- Finner is an orca who is proud of having the skill of surfing, and has a love interest in Manette (not in CRF). he usually dies by either getting himself impaled by his surfboard, drowning uncontious or getting burned. Finner is a new character in the show, meaning he has not appeared in a episode (yet).
- Generic Reef Friends are random characters who take on multiple personalities and aquatic species. Young GRF's are often found in schools.
- Coral the Merfox can be spotted in the background in some episodes.
- Russell can be spotted sailing or fishing.
- Marlin can be seen swimming around.
- Chenspurr can be seen battling ninja GRF's in the background.
- Raymond can be seen swimming around.
- Fish Stick can be seen fishing with Russell.
- Bruiser can be seen bullying GRF's
- Eejit can be seen swimming around.
- Pancake can be occasionally seen either drowning or just swimming.
- Manette can be seen kissing pictures of Finner in the background.
- Crabby tries to escape from their chains by cutting it with a shell while Goof has drowned.
- A few broken pieces of Cream are seen falling in the water.
A book is shown to be opening, decorated with shells that spell out "Coral Reef Friends". Then, the underwater city pops open like a pop up book, followed by the creator and developer names with letters in bubbles. Then the book closes and a hand grabs it, revealing the book to be laying sideways on a fish tank, and the camera tilts slightly, zooms in, and the characters do an idle in the bed of aquarium sand.
- Fisher's Day: It's fishing day, and the main fishing targets get revenge on the fishermen.
- Reef Sale: Sparkle finds out his parents are hosting a garage sale.
- Battling Seafriends: A battle between Hingy and Quacks goes under way.
- We'll Never Be Oil: An Oil Spill affects the habits of the Coral Reef Friends.
- Pungent Sponge: Overbite mistakes Spongy for cheese and eats him. Now Spongy regrows - inside the shark's body!
- Undef-eatable: A shortage on food leaves the Coral Reef friends at the bottom of the food chain.
- That's a Stinger!: Stinger gets more than he bargained for when he decides to bully Chuckly.
- Brain Mush: Mush takes over the world with his army.
- Scaredy Squid: Oily has a nightmare, and doesn't want anyone to know about his fear. (Halloween special)
- The Urgent Urchin: Urgent tries to run errands, but finds a solution to make things faster.
- Diver Dozen: Unfortunately for the CRF's, Splashy is looking for them to turn them into seafood.
- Soda Pop Stopped: A six-pack ring causes trouble in the habitat of the Coral Reef Friends.
- Claw Massage: Claw tries to be a masseuse. There are more deaths than there were happy customers.
- Stuntflush: Blasst jumps over a pile of toilets as a stunt, but misses and gets stuck in one of them.
- Chuckle Nuts: Laughy tries the classic eel-in-a-can-of-seanuts prank with Teary, and now he wants to kill him.
- Caviar or Can't: In the Season 2 premiere of CRF, Sparkle steals some eggs from a nest after mating time after he hears that some caviar are worth a lot of sand dollars. However, he is unable to protect it himself, and one gets lost. Luckily, Delicious finds one of the caviar.
- Holey Mackerel: Mackey tries to start a new religion where HE is the god.
- In a few episodes, you can see a generic normal-colored goldfish with three eyes. This is a reference to The Simpsons.