The second season of the Bear in the Big Blue House series began airing from June 1st, 1998 to February 1st, 1999. It contains thirty-nine episodes.
- Ooh, Baby, Baby - Bear helps Tutter learn how to care for a baby.
- Raiders of the Lost Cheese - The gang look for the lost cheese.
- The Big Sleep - Ojo, Treelo, Tutter, Pip, and Pop have a sleepover in the big blue house.
- Clear as a Bell - Bear talks about communicating.
- Good Times - Everybody wants time with Bear.
- You Learn Something New Every Day - Bear receives a notice in the mail.
- Back to Nature - Everyone talks about nature.
- The Ojolympics - Ojo gets the idea to start The Ojolympics.
- The Great Pretender - Bear shows Tutter that he's better at pretending than he thought.
- It's All in Your Head - Bear is planning to take the kids of the Big Blue House to the fair.
- Oops, My Mistake - Bear accidentally receives a piece of Doc Hogg's mail and decides to call him and let him know about it.
- Bear's Birthday Bash - Ojo, Treelo, Tutter, Pip, and Pop decide that they should give him a surprise party.
- Picture This - Bear decides to take some pictures of things around the Big Blue House and make an album to send to Ursa.
- The Big Blue Housecall - Doc Hogg pays a special visit to the Big Blue House to give everyone a checkup.
- Change Is in the Air - Bear has been planning on a visit from Doc Hogg, but finds his plans disrupted when a spate of colds at the swamp forces Doc Hogg to change his plans.
- Look What I Made - At the Big Blue House, Bear finds that his friends are all making inventions.
- If at First You Don't Succeed... - When Ojo decides to pretend that she's a big bear, Bear invites her to join him on a berry-picking expedition at the Otter Pond.
- All Weather Bear - Bear and his friends have decided to go swimming out at the Otter Pond.
- I Built That! - Bear recieves a birdhouse kit in the mail and he's excited about building it.
- Tutter's Tiny Trip - Tutter is nervous when Grandma Flutter plans to take him on a trip outside the Big Blue House.
- Dance Fever! - Treelo wants everyone to dance.
- Afraid Not - A thunderstorm comes which causes the kids to become scared.
- I Gotta Be Me! - One day in the Big Blue House, Bear finds himself trying on new clothes, hoping to come up with a new look.
- Buggin' - Bear and his friends talk about insects.
- Love Is All You Need - Bear is having a hard day. He misses Luna, who he loves very much.
- It's a Mystery to Me - When Bear pays a visit to the Otter Pond, he gets the first word of strange events happening in and around the Big Blue House.
- As Different as Day and Night - Bear talks about opposites.
- Grandparents Just Want to Have Fun - Pip & Pop can hardly wait for their grandma Etta and grandpa Otto to visit.
- The Way I Feel Today - The gang of the Big Blue House find themselves feeling many different ways and Bear is there to help sort it out.
- You Go, Ojo! - Bear and Ojo talk about the many great things that a girl can do.
- Scientific Bear - When Tutter decides to investigate new uses for Swiss cheese, Bear suggests a scientific experiment.
- Boys Will Be Boys - Bear and his friends talk about boys.
- I Was Just Thinking - Bear has received a book of brainteasers and is eager to try some of them.
- Wish You Were Here - When Grandma Flutter takes the children of the Big Blue House out to a square dance, Bear plans a day of busy activities. Instead, he finds himself missing their company.
- And to All a Good Night - There's a special party out at the Otter Pond and Luna even has a special surprise for Bear.
- Call It a Day - Bear and the kids have had a busy day and are now turning in for the night.
- We Did It Our Way - Bear talks about cooperation.
- What's the Story? - Bear gets ready for the Annual Woodland Valley Storytelling Festival at the Big Blue House.
- When You've Got to Go! - Bear talks about how to use the bathroom.
- The airings of the episodes of this season are not in order. So the the episode Look What I Made aired on Christmas Eve. That episode was the last episode to air.
- This season has the most episodes in the series.