Blue's Clues was designed and produced on the assumption that since children are cognitively active when they watch television, a television program could be an effective method of scientific education for young children by telling stories through pictures and by modeling behavior and learning. These learning opportunities included the use of mnemonics in the form of mantras and songs, and what Tracy called "metacognitive wrap-up"
The thinking games presented in each episode used what Anderson called "a layered approach" that took the varying capabilities of the audience into account. Santomero said that they used scaffolding and that layering was inherent in the script and design of each game. They purposely presented the problem presented in increasing levels of difficulty, to prevent children from feeling frustrated and to master concepts, experience success, and feel empowered to attempt to solve more challenging concepts presented to them. The producers' goal was that all viewers understood the problem, even if they did not know how to solve it. As a result, the child was temporary frustrated by not knowing the answer because after giving them time to come up with it, child voice-overs provided the answers for them, so that they learned the correct answers, even if they were unable to come up with them. If the child was able to come up with the answers, however, they felt "part of a larger, knowing, child audience" this was done was in the use of pauses that were "long enough to give the youngest time to think, short enough for the oldest not to get bored". The structure of each episode was repetitive, designed to provide preschoolers with comfort and predictability.
Since preschoolers tend to have difficulty understanding transitions, especially when they involve active inferences about time, space, and characters' perspective, the program's producers minimized transitions that required inference so that their viewers' intellectual resources could be devoted to understanding the episode's content. They accomplished this goal by limiting the number of settings during an episode and with the transitions occurring only between them and signaled by dialogue and enough time and information necessary to process them. The primary settings in Blue's Clues were the host's house and backyard, and transitions between them were usually done continuously, without the use of cuts. If transitions were accompanied by cuts, it was done by the host moving to and through a door and continuing as he entered the front or backyard. The biggest transition in Blue's Clues occurred when the host "skidooed" and jumped into a picture or book, done in a magical way with plenty of warning that it was coming, and began and ended in the new environment. Anderson reported that children clearly understood and enjoyed the skidoo transition. Santomero reported that the skidoo transition was inspired by the use of the trolley in Mister Rogers' Neighborhood, which also served as a transition device.
According to Dhingra and her colleagues, the researchers represented the preschool viewer. After coming up with an idea for an episode, the writers met with Alice Wilder, head of the research department for Blue's Clues, to discuss their idea. The research department and writers then discussed if the topic and approach to the topic was appropriate for preschoolers, and if they accepted it, the content of the episode was further developed. They would often bring in outside consultants who were experts in the subject matter and the processes in teaching it to preschoolers. Wilder considered the researchers experts in how the concepts they wanted to present would translate to the medium of television rather than in a classroom or museum, but they considered preschoolers, who evaluated each script from their perspective, to be their " true experts". The writer took the information they gathered from the research department, preschoolers, and experts and wrote a treatment, or detailed outline of the script, which included goals for the entire episode and for each game. The writers, Wilder, and the research team had a treatment meeting, which Dhingra and her colleagues described as "an organized creative brainstorm", which was rooted in the philosophy and mission of the show, the art of good storytelling, and the point of view of their viewers. The goal of the treatment meeting was to give the writers everything they needed to create a workable second draft of the episode script, and to ensure that it fit the needs of their viewers. The producers and creators of the show, during their interviews of preschoolers, created a rough version of the episode, with the host and preliminary animations and backgrounds, and showed it to preschoolers to gain further feedback and was designed to assess their reactions to the content and visuals. According to Dhingra and her colleagues, the greatest strengths of the development of all episodes of Blue's Clues were the high levels of collaboration between all departments involved in the creation of the show, the clearly defined strategies they used to effectively include their preschool viewers in the development process, and their use of the mission, philosophy, and structure of the program to create and develop each episode.
Most of the show's production was done in-house, rather than by outside companies as was customary for children's TV shows at the time. Blue's Clues was filmed in a studio in Tribeca, Manhattan, New York. The show's creators understood that the look and visual design of the show would be integral to children's attachment with it. Johnson expanded on the "cut-out" style she had created during her college years. Blue's Clues was the first animated series for preschoolers that utilized simple cut-out construction paper shapes of familiar objects with a wide variety of colors and textures, resembling a storybook. Johnson also used primary colors and organized each room of the home setting into groups. The green-striped shirt worn by the show's original host, Steve, was inspired by Fruit Stripe gum. similar to picture book illustrations. The program's design was influenced by an understanding of the cognitive, emotional, and social capabilities of preschoolers. For example, the purpose of the notebook in Blue's Clues, which was used to record the clues presented throughout an episode, was to teach preschoolers how to overcome their poorly developed memory skills by using external mnemonic aids and lists. The music, produced by composer Michael Rubin and pianist Nick Balaban, was simple, had a natural sound, and exposed children to a wide variety of genres and instruments. Rubin and Balaban used Anderson's research about the importance of using auditory cues to increase children's attention and inserted auditory signatures to encourage the audience to pay attention to the episodes "at critical junctures for learning".
The host performed each episode in front of a "blue screen", with animation added later. Johnson hired artist Dave Palmer and production company Big Pink to create the animation, which was at that time a new technology, from simple materials like fabric, paper, or pipe-cleaners, and scan them into a Macintosh computer so that they could be animated using inexpensive computer software such as Media 100, Ultimatte, Photoshop, and After Effects.