Updated: March 08, 2013

The second season began with a trip inside a whale, a trip inside a volcano, and a few Cold War intrigue and nuclear war-themed episodes, and saw several brushes with world disaster. The season ended with a ghost story, one of the show's few sequels.

Due to ABC's demands for a somewhat "lighter" tone to the series, the second season saw an increase in monster-of-the-week type plots, yet there were still some episodes that harkened back to the tone of the first season. The second season also saw a change from black and white to color. The beginning of the second season saw the permanent replacement of Chief "Curly" Jones with Chief Sharkey, due to the death of Henry Kulky, who portrayed Chief Jones.

The most important change in the series occurred during this season when a slightly redesigned Seaview was introduced, along with the Flying Sub. The Flying Sub was a yellow, two-man mini-submarine with passenger capacity, that could leave the ocean and function as an airplane. The Flying Sub was referred to by the initials FS-1. The futuristic craft greatly increased Seaview crews' travel options. The Flying Sub was launched from a bay in the lower part of Seaview that was apparently built between Seasons One and Two. The Seaview's private observation deck from the first season was never seen again. The Seaview's eight observation windows became four. The Seaview's enlisted men were also given more colorful uniforms (red or light blue jumpsuits), evidently to take advantage of the changeover from black and white to color. The officers and petty officers, however, retained their khaki works from the first season. The traditional sailor uniforms worn in the first season were only seen in stock footage from the first season and on characters who were newly filmed to match up with that footage. All these changes occurred between seasons. The Flying Sub was showcased in the show's closing credits for the entire season.

The "Flying Sub" also made an appearance in the 1971 Irwin Allen film, City Beneath the Sea (1971 film) (as did the Seaview itself during the evacuation scene).

A second season episode, "The Sky's On Fire", was a remake of Irwin Allen's 1961 film Voyage to the Bottom of the Sea.