According to series creator Ed Annunziata, he originally planned to name Ecco the Dolphin after the dolphin constellation Delphinus (a design that appears on Ecco's head in the form of scars). Sega of America's global marketing director Al Nilsen instead suggested the name Botticelli, referencing the Renaissance painter Sandro Botticelli, in an attempt to imitate how the Teenage Mutant Ninja Turtles were named after famed Italian artists. Annunziata sensed this was a bad idea and turned to Sega of America's director of product development Clyde Grossman, who suggested "Echo" based on echolocation. Annunziata then replaced the "h" in the name with a "c" to form the final name; he explained that it was a reference to the Italian word "Ecco", which can be loosely translated to English as "I see" (i.e. understanding something). It is also thought to be a reference to the works of John C. Lilly, a neuroscientist known for his controversial attempts to communicate with dolphins, who believed that he had been contacted by an alien organization called the "Earth Coincidence Control Office", or "E.C.C.O." While this connection has not been directly confirmed, Annunziata once stated in a series of tweets about Ecco the Dolphin trivia that he "never took LSD, but did read a lot from John Lilly".

Ed Annunziata, the game's head designer, cited English progressive rock band Pink Floyd as a major influence on the game's music. The band's 1971 song "Echoes" may be the origin for the protagonist's name, and one of the game's final levels, "Welcome To The Machine", may be a reference to the band's 1975 song of the same name.

Most of the artwork in the prehistoric era looks very similar, if not identical, to scientific artwork by Zdeněk Burian.

In Origin Beach, there are two glyphs that are behind the walls in the top left and right corners of the level. These were put in by the developers to answer the question "Why do dolphins live in the sea?"

The left one says:
We hear song in the ocean!
We hear our kind in the sea!
Never have we heard songs in the sea!

The one on the right says:
You sing our song under the waves
Who are you?
Could we sing in the sea?
Could we live in the sea?
Perhaps we will try!

Ecco the Dolphin creator Ed Annunziata stated that he made the game so hard because he was paranoid that kids would rent the game and beat it over the weekend.