Jupiter, Pete, and Bob live in Rocky Beach, a fictional southern California coastal town described as 10 to 12 miles from Hollywood and 15 miles from downtown Los Angeles. Jupiter's family owns and operates the Jones Salvage Yard ("the Yard"), where the team's headquarters is hidden in an old trailer, which itself is hidden amid the "junk." There are several ingenious secret entrances (ie. Tunnel Two, Door Four...etc). The trailer's equipment includes a telephone, a darkroom, a filing cabinet, and a workshop in which Jupiter assembles devices, mostly from discarded items found in the junk yard, which help the Investigators in their detective work. The team often has to pay for what they take by working for Aunt Mathilda, a hard taskmaster who believes "idle" boys should be put to work.

Jupiter has designed a business card to intrigue their potential clients, memorable to readers particularly for its three question marks. These potential clients often ask what the question marks stand for, giving Jupiter an opening to impress them with his explanation that they are "symbolical of questions to be answered, mysteries to be solved." The boys' patrons usually did no more than introduce them to cases, meet again with them at the end of a particular adventure, and sometimes refer them to specialists such as a scholar on studies of the supernatural. At no point is it ever suggested that the patrons provided the Investigators funding in their work.

The Three Investigators solve cases by doing research (Bob's speciality), active observation (Pete's speciality), and clever deduction (Jupiter's speciality). Though the boys are both younger and lack the resources and connections of fellow fictional detectives The Hardy Boys and Nancy Drew, they have found ways to compensate or ignore these handicaps. Though too young to drive, the Three Investigators soon acquire reliable transportation in the form of a Rolls Royce limousine driven by British chauffeur Worthington. Jupiter won the use of the limousine for "thirty days, of twenty-four hours each" after winning a promotional contest held by the rental agency, soon before beginning their investigation of The Secret of Terror Castle. Despite Jupe's argument that the wording "thirty days of twenty-four hours each" meant that the boys should have the use of the Rolls Royce for the equivalent of 30 full days (or 720 hours), the Rent-N-Ride Auto Agency briefly ended their use of the limo in The Mystery of the Fiery Eye. Fortunately, a grateful client arranged for the boys to have access to the car whenever they needed it. Nevertheless, although Worthington became a confidante and a supporter of the boys' work, the limo's use grew rare in later books.

After proving their reliability, the Investigators received a green card from Rocky Beach police chief Samuel Reynolds, which identified them as junior deputies cooperating with the Rocky Beach police. They used this credential occasionally to convince others they were serious detectives.