Based on the popular books by Marcus Pfister, the animated series follows the adventures of a boy fish with glittering scales and his friends in the underwater Bay of Neptune.
Sea Filly the Sea-horse, comes to the school of fish, and Rainbow and his best friend Blue, welcome her in.
Rainbow is excited to meet his hero, renowned hockey star Wayne Grunion when he comes to town for a visit.
In the school band, Mrs Chips gives Rainbow Fish the conch shell, the hardest instrument in the band to play. Rainbow is then forced to practice, and he does so, gradually making for a better performance at the school concert.
When Rainbow Fish and his friends attempt a dangerous sport called "Riptiding", Blue is swept away on a riptide, and Sea Filly and Rainbow must find him before it's too late.
Rainbow Fish gets a bad report card (he gets a "C"). But when he accidentally spills ice cream (from a kelp gusher milkshake) on it at Wanda's, his parents mistake the "C" grade for an "A". Rainbow must prevent them from meeting Principal Gefilte and learning the truth. For getting a "C", changing his grades, and lying that he got an "A", he is cave grounded by his parents until he gets his grades up. This means until he gets his grades up, he is "cave grounded" except for school (meaning he can only leave the house to go to school while cave grounded).
Rainbow is not enthusiastic about spending time with his grandpa while his parents are away at the store, thinking that he will be bored, but when his grandpa tells him an amazing story that hides an incredible secret, Rainbow discovers that old people can be exciting after all.
Rainbow fears visiting the dentist, but when he goes, he discovers that dentists are not as bad as he thought they were.
Rainbow mistakenly brags to his friends that he knows the famous pop star, Bruce Sturgeon, which lands him in trouble and causes him to force Bruce Sturgeon himself to perform at the school.
A new student, Sherman Shrimp, comes to school and Rainbow Fish treats him badly. However, after Sherman saves Rainbow from a sudden shipwreck, Rainbow realizes that he has been bad to Sherman all along.
Chomper, the school bully, gets lost in a canyon along with Rainbow Fish, and the two opposites must work together to find their way out.
Rainbow fools around with his father's golf club and breaks it, causing him to search for a new one before his father's big game with Sir Sword.
Ruby decides to babysit their guppy neighbors' baby, Ferdie, and says Rainbow is too irresponsible to help her. However, Ferdie turns out to be more troublesome than expected and swims away. Rainbow then finds him and Ruby apologizes for what she said.
Sir Sword needs to finish third grade, so he attends Rainbow's school, the School Of Fish.
Blue has a crush on Goldie, but he's too shy to ask her on a date, so Rainbow tells him what to say via a communicator made by Sea Filly. However, Chomper and Stingo soon ruin the plan.
When Blue becomes a hall monitor for the School Of Fish, he lets the power go to his head.
Blue gets a new baby sister, and he feels left out, all because of the attention his mum and friends are giving to the baby.
Rainbow lines a sea-monkey bowl with his sister Ruby's magazine, ruining the magazine itself in the process.
Rainbow learns a lesson about charity and works on a project involving just it.
Ruby starts spending time with Rainbow, Blue and Sea Filly the sea-horse, leading Rainbow to believe that she is trying to steal his friends.
Rainbow gets a job at the Candy Counter to earn money.
Rainbow takes up making movies, thanks to a new waterproof camera, and casts himself as Director.
Rainbow's pen pal is coming to visit him, and Rainbow is excited about it.
Sea Filly becomes the editor of the School Of Fish newspaper. Unfortunately, in her enthusiasm for journalism however, she soon becomes nothing but a tabloid gossip columnist and no fish is safe from her probing and humiliating articles. Rainbow comes up with a plan that ends with Sea Filly writing a false article about Principal Gefilte and losing her job. Sea Filly soon learns that real journalists have a responsibility to print only what they know is true.
In spite of some ongoing construction taking place outside the School Of Fish causing a big deal of noise, Rainbow is sent home early and gets freedom. A pair of burglars soon break into the Fish cave, and try to ruin it any way they can, all while Rainbow watches his favourite cartoon, "Silly Salmon" on TV by himself. Thanks to a 911 call being traced, Rainbow arrests the burglars and saves the day, pleasing Aqua and Sol in the process.
Rainbow and Blue start hanging out with a new clique called the High Tides, due to the chagrin of Sea Filly.
Sir Sword lends Rainbow a book that he becomes hooked on and cannot stop reading.
When Ruby encounters a series of unfortunate events one day, she believes that she has been cursed.
Rainbow's class has Dads' Day at school and all students' fathers are invited to describe their own, personal jobs. Rainbow is worried, however, as he thinks his father has a boring job.
Rainbow finds a hole in the ground that an extinct coelacanth called Carl swims out of. However, Carl spends most of his time in the modern world, trying to impress Ruby. This might be a reference to another Marcus Pfister book, called Dazzle the Dinosaur.
Rainbow and Blue compete for the role of class president. They both try to impress Sea Filly in order to get her vote.
Blue wins the clamball championship for his school, but only because no one sees him drop the ball anywhere.
Rainbow is suspicious of his sister, Ruby, when she starts acting very strangely. However, it turns out, that she is just making a surprise gift for their parents.
Rainbow's mother, Aqua, invites his teacher, Mrs Chips, to dinner, and Rainbow Fish is worried that Mrs Chips herself will act just like a teacher.
One difficult day, a glowing guardian angel fish shows Rainbow Fish the value of his life.
Rainbow Fish fears that both his parents, Sol and Aqua, are planning to sell the cave to two fish called Ret and Snapper, and so his friends attempt to make his house as much of a wreck as possible to avoid it being sold. However, Rainbow then discovers his parents were planning to build a new recreation room.
Rainbow and Ruby prepare an anniversary dinner for their parents.
Rainbow saves a whale's life, and, in return, the whale (Leslie David Baker) becomes his bodyguard.
Rainbow is not pleased when his mother, Aqua, gets a job in his school.
After being teased by her classmates for not being feminine enough, Sea Filly decides to take up cheerleading, causing Blue and Rainbow to worry about her becoming a different person altogether.
Rainbow is embarrassed after failing to stand up to Rocko Rockfish (Alan Marriott), a bullying second grader.
After watching Rainbow and Blue play it in Shipwreck Park, Sea Filly becomes addicted to a 2000 computer game called "Clam Blaster" and hardly does anything else. However, when she brings the video game to the School Of Fish one day and plays it there during a difficult maths test with Mrs Chips, she soon discovers that the video game itself is "dumb, violent and intellectually worthless".
Rainbow, Blue, and Sea Filly hear the tale of two feuding crabs who were once song-and-dance partners, and then, they all set out to bring them back together, once and for all.
Sea Filly gets a bad grade on a maths test at the School Of Fish and worries greatly.
When Blue looks at his book and mistakenly thinks that his ancestors were royalty, he starts acting like a prince.
When Chomper's cousin Slick (Macaulay Culkin), a pool-playing master, comes to Wanda's refreshment shop, he beats everyone in Pool by secretly cheating. Rainbow, unaware of this at first, is in awe, and decides to become his assistant, then discovers his secret. Rainbow then declares a match to determine that Chomper's relative is cheating. Rainbow then wins, and the other player leaves the shop forever.
Rainbow tries to put Sea Filly in the Halloween spirit, but then has a haunting Halloween dream, and wakes up to find that Sea Filly has actually scared him in his sleep.
Phineas T. Gronch is planning to permanently demolish the Mollusk Reef Villas as well as wipe out half of Neptune Bay to build a shopping mall in its place. Rainbow, Blue and Sea Filly have to stop him in time, or they'll all be for it.
Rainbow and his family go on a camping trip.
Important friendship is tested when Blue comes to stay in Rainbow's cave.
Chomper is given the lead role in the school play, but he mistakenly believes that voice acting is for wimps.
