A new girl, Sea Filly (who is a seahorse) comes to Rainbow Fish's school and Rainbow and his best friend Blue welcome her.
Rainbow is excited to meet his hero, renowned hockey star Wayne Grunion when he comes to town for a visit.
In the school band, Rainbow Fish is assigned the conch shell, the hardest instrument in the band to play. Rainbow is then forced to practice and he does so, 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 his friends must find him.
Rainbow Fish gets a bad report card (he gets a "C"). But when he 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 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 aren't 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 shipwreck, Rainbow realizes that he has been bad to Sherman all along.
Chomper, the school bully, gets lost in a canyon 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 runs 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.
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, he lets the power go to his head.
Blue gets a new baby sister and he feels left out because of the attention his mom and friends are giving to the baby.
Rainbow lines a sea-monkey bowl with his sister Ruby's magazine, in process ruining the magazine.
Rainbow learns a lesson about charity and works on a project involving it.
Ruby starts spending time with Rainbow, Blue and Sea Filly, leading Rainbow to believe she is trying to steal his friends.
Rainbow gets a job at the Candy Counter to earn money.
Rainbow takes up making movies and casts himself as the director.
Rainbow's pen pal is coming to visit him and Rainbow is excited.
Sea Filly becomes the editor of the school 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 an untrue article about Principal Gefilte and losing her job. Sea Filly learns that real journalists have a responsibility to print only what they know is true.
Burglars break into Rainbow's house one afternoon and ruin it.
Rainbow and Blue start hanging out with a new clique called the High Tides, 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 jobs. Rainbow is worried, 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 may be a reference to another Marcus Pfister book 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 saw him drop the ball.
Rainbow is suspicious of his sister when she starts acting oddly. However, it turns out she is just making a surprise gift for their parents.
Rainbow's mum invites his teacher, Mrs. Chips, to dinner, and Rainbow is worried that she will act like a teacher.
A guardian angel fish shows Rainbow the value of his life.
Rainbow fears his parents are planning to sell the house 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 becomes his bodyguard.
Rainbow is not pleased when his mother 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.
Rainbow is embarrassed after failing to stand up to Rocko Rockfish, a bullying second grader.
After watching Rainbow and Blue play it, Sea Filly becomes addicted to a video game called Clam Blaster and hardly does anything else.
Rainbow, Blue, and Sea Filly hearing the tale of two feuding crabs who were once song-and-dance partners, and set out to bring them back together.
Sea Filly gets a bad grade on a math test and worries greatly.
When Blue looks at his book and mistakenly thinks his ancestors were royalty, he starts behaving like a prince.
When Chomper's relative, 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, then has a haunting Halloween dream, and wakes up to find Sea Filly has scared him in his sleep.
Phineas T. Gronch is planning to demolish the Mollusk Reef Villas and Neptune Bay to build a shopping mall. Rainbow, Blue and Sea Filly have to stop him.
Rainbow and his family go on a camping trip.
Blue and Rainbow's friendship is tested when Blue comes to stay at Rainbow's house.
Chomper is given the lead role in the school play, but he mistakenly believes acting is for wimps.
Rainbow's love of kelp gusher drinks causes him to get hiccups.
Rainbow Fish helps Sir Sword dressed as Santa Sword on Christmas Eve.