Episode 1

Bea, one of the three fish BFF's including Milo and Oscar at Fresh Water High, freaks out literally when her annual school photo is taken, for she claimed that it was taken badly. In the attempt to bring it back fearing that her expected future as an actor would be in jeopardy by a single bad picture, she distracts her friend and school photo editor Pirahnica, who claims to be in love with Oscar, by making the poor fellow take her on a date. After avoiding dangerous obstacles set by Pirahnica, Bea and Milo find the pictures as they see Bea's taken one. Milo discovers that there was nothing wrong with it. Bea had known that, but she thought that her look wasn't suited for an actor. After Milo talked some sense into Bea by proclaiming that she was perfect the way she was, she suddenly remembers Oscar and stops his nightmare with Pirahnica by stating that she and Oscar were dating. After the nutty clam left, Oscar was happy that Bea felt the same love he felt for her, only to figure out that she was acting.

Episode 2

Bea has a girl sleepover party and Milo and Oscar feel left out, so attend the party as Milina and Oscerlisabeth. Chelsea and Bea let the other girls know that they are Milo and Oscar. But instead of confronting them, the girls then make them do what girls really do on sleepover parties.

Episode 3

Milo ventures out of the fish tank alone, so Bea and Oscar follow him. The three best friends catch the eye of the pet store cat Wilfred, and Milo must put aside his differences with the others to save the day.

Episode 4

When Bea goes on several dates and Milo gets a date, Oscar feels he is the only one without a girl so and pretends to have a girlfriend named Doris Flores Gorgeous, but he struggles to keep it a secret from Milo and Bea. He tells Milo and Bea that Doris lives in Fish Niagara Falls so the friends try to "cheer up" Oscar by taking him there. When they get there, there actually is Doris who turned out to be Clamantha.

Episode 5

Milo tries to follow his dream by playing on the Football team but gets the job of Water Boy. Little does he realize the importance of his job, since the football team is playing at the Gecko tank.

Episode 6

When Jocktopus's birthday comes up, he warns every student in freshwater high that if they don't bring a gift for him, they will get "pounded" by him. When shopping for said gift Oscar suggests getting him money, which results in Oscar himself being given as a gift by his friends who don't want to be pounded. Bea and Milo try to get him back.

Episode 7

Bea decides to take a job at Fish Flakes but soon misses her old carefree life, but no one will let her quit. Meanwhile, Milo and Oscar get sent to daycare after being mistaken of being Bea's babies. Oscar dislikes the babies, but Milo wears a diaper and stays nearby.

Episode 8

Milo and Bea get a dog named Murphy, who Oscar doesn't like. Oscar ends up yelling at the dog and as a result the dog runs away. Now Bea, Milo, and Oscar will have to go and find Murphy.

Episode 9

When the school homecoming dance is coming up, Bea must be chosen to be Homecoming Queen. But her "embarrassing" parents have signed up to be chaperones. So Milo and Oscar help plan a fake school dance to stop them from ruining Bea's chance at becoming queen.

Episode 10

Bea and Oscar help Milo study for his final exam so he doesn't get held back a grade like their old friend Kevin. To do this, they must find Milo's un-traditional way of learning.

Episode 11

Oscar seems to be the only one without a good sense of humour, so Milo and Bea tell Oscar to just pretend everything's funny. But he goes too far.

Episode 12

Oscar and Milo believe that their teacher Mr. Baldwin lives a double life as a comic book superhero and Bea, who needs to do a report for Dr. Frog's class. He tells Bea that they have to get proof.

Episode 13

Milo and Oscar search for new roommates after they fight over Milo's messy habits.

Episode 14

Oscar has an accident and wakes up in what he believes is his fantasy novel. Meanwhile, Milo and Bea try to find Oscar, but runs into different kinds of fake Oscars.

Episode 15

Milo, Oscar and Bea travel to Hamsterwood where Bea can have her own TV show. However, there is something fishy going on in there, and it turns out the hamsters are planning to eat Bea!

Episode 16

Milo finds a siamese fighting fish ninja and uses his skills to intimidate Jocktopus from bullying. However, the power quickly goes to Milo's head, and he begins to punish everyone by trapping them in glass bowls for ridiculous reasons.

Episode 17

When Albert Glass becomes sick with the dropsy and is given plenty of attention, Milo decides to fake being sick in order to get some for himself.

Episode 18

Bea is friends with everyone except Albert, who doesn't like her. Bea takes it upon herself to get him to be friends with her at any cost.

Episode 19

When Oscar believes nobody understands him, he joins a group of goth fish and changes his name to Bubblethorn. So Milo and Bea try to get Oscar back from Razor and the goth fish.

Episode 20

When Milo is very weak in Bea's class, Coach Samons tell him to exercise. Since Milo is lazy, he gets help from Jumbo Shrimp and uses a tank to make him stronger. He gets careless and gets bigger and stronger which he turns into a monster.

Episode 21

Milo does not have any money, unlike Oscar and Bea. They tell him to work but he is lazy and stubborn so he loans money from Randy Pincherson and then Randy treats him he is going to pinch Milo because he used up all the loan. Oscar and Bea give their money to Randy and become very angry with Milo, abandoning him as a friend. Milo decides to work but at the job, he thinks it is very hard just to put the cash into the register. He has the money for the tickets to a concert and the money he owes to Oscar and Bea.

Episode 22

When Principal Stickler says that the boys would build a float and the girls will build another, It becomes a fight because Milo did not come up with a plan and plans one of the boys to spy on them. When the boys and the girls show tier floats, it collapses and becomes a Principal Stickler Float.

Episode 23

After Mr. Mussels gives an inspiring speech about going after your dreams, Milo ends up finding his dream in an actual dream … he wants to fly across the pet store! Bea and Oscar are certain that this is just a Milo moment, but realize he’s serious after Milo decides to trap a bird to fly on.

Episode 24

When Clamantha’s crush on Oscar begins to overwhelm him, he thinks his problems are solved when she develops a crush on his laptop, mistaking it for a fellow clam. When the battery starts to die, Clamantha is upset that her new boyfriend is ignoring her and Oscar must find a way to make things right.

Episode 25

Milo entertains holding onto Bud's ear with a fishing pole attached to the end of a plunger, but then shoots into the pocket of his shirt. Milo now runs the risk of becoming dehydrated.

Episode 26

Oscar tries to get Milo involved in recycling, but Milo goes overboard when Oscar comes up with a "fake" story and tells Milo about a Magical Earth Troll.

Episode 27

Milo sees a horror movie and thinks fish brain parasits are infecting everyone.

Episode 28

When Pamela Hamster visits Milo in Freshwater High, Oscar and Bea are in trouble.

Episode 29

Oscar takes his driving test, but things get wild when his driving instructors turn out to be Mr. Mussels and Coach Salmons.

Episode 30

Milo comes up with a great idea: fridge hats. But when Randy Pincherson mysteriously starts selling fridge hats and claiming he came up with the idea, Milo and the others must figure out how Randy knew the idea and how to expose him.

Episode 31

Oscar bores everyone in Freshwater High School with his morning announcements, so Bea helps make the show more entertaining, but after Oscar realizes that she starts making the morning announcements not about school and decides to quit, but doesn't get his chance to announce the cafeteria being closed for repairs.

Episode 32

Randy Pincherson steals Bea's diary and blackmails her to go on a date with him. In order to get her diary back, she goes on a date with Randy. Milo and Oscar steal Randy's diary.

Episode 33

Milo and Oscar dress as the school's mascot, but when the fame-happy Milo exposes them, not only does he embaress his shy brother, but players from a rival school kidnap Oscar to destroy Freshwater High's moral for the championship.

Episode 34

Oscar discovers his college dreams and aspirations are put in jeopardy because of his lack in extracurriculer activities, so Bea and Milo try to find Oscar the perfect club, and find Clamantha fighting with her arch-nemesis, Clamanda, and Milo, Oscar, and Bea's friends join Clamantha's cheerleaders team after her team gets brought by humans, but Bea turns out to be in Jumbo Shrimp and Albert Glass' map club so she is unable to help out the team. This is a two-parter, Disney lists as episodes 133 & 134

Episode 35

Oscar is being honored with an award for perfect attendance and, unfortunately, Bea and Milo get the trio into a predicament, preventing Oscar from being there, but Oscar is determined to make it back on time and get his award.

Episode 36

The class is on a field trip to PuPu Goodtimes Amusement Park and Bea, Milo and Oscar all have individual goals in mind. Bea is determined to get on a ride with Steve Jackson, Milo is embroiled in a macho man "ride-off" with Randy Pincherson and Oscar joins forces with Jumbo Shrimp and Albert Glass to win a Galactic Fish Battles Limited Edition Fork Saber. It's all fun times at PuPu Goodtimes!

Episode 37

Oscar's impression of the Queen of Fish England is so similar that even Mr. Mussel's, who is a big admirer of the Queen, cannot tell the difference. The gang goes along with the ruse, until Oscar is mistaken for the Queen by a bridal party and swept away to "his" royal wedding. The day then escalates into a "Slow Jams Rap Battle" between Milo and Mr. Mussels to win the hand of the fair Oscar.

Episode 38

After Milo accidentally rips Bea's new red dress for the school dance, he and Oscar find another copy of the dress, but it costs 1,000 fish dollars. To raise the money to buy the dress, they get jobs at the store so they can use their salaries to buy it.

Episode 39

Jocktopus reveals that it is his father's dream for Jocktopus to sing in a musical play about potatoes. So during the Freshwater High musical play, "Potatoes In Winter," He goes in the play to sing but gets nervous. Note: This is in two parts, usually listed as episodes 138 & 139. Disney still lists this as the season final, even after showing 3 more episodes after it.

Episode 40

It's Halloween in Freshwater, and the gang is eager to get boatloads of candy, but Jocktopus is beating trick-or-treaters up and stealing their candy. To get their sweets and not get beaten up by Jocktopus, they journey outside the tanks to trick-or-treat. It's going to be a wild Halloween for Milo, Oscar, and Bea! Note: This was originally scheduled to be episode 201.

Episode 41

The talent show is coming to Freshwater and Bea is determined to win. But the talent show turns into a battle when Clamantha gets into a fight and the entire school is divided into the non-participants and the performers. Can the gang stop this talent tragedy?