Before the building of the attraction, the Rainbow River was known at different times as Wekiwa Creek or Blue Run. 'Rainbow River' seemed more marketable and the names of the river and springs were changed to the names they bear today.

The Rainbow River in Dunnellon, Florida, was named for the stunning prismatic effects created by the interplay of sunlight and its crystalline, spring-fed waters. As described in historical accounts dating back to 1891, the water is so clear that when light hits the diverse underwater vegetation and limestone vents, it creates a "rainbow" of colors on the riverbed. This visual phenomenon is most prominent at the headwaters, Rainbow Springs, which is a first-magnitude spring discharging nearly 400 to 600 million gallons of water daily. The name was further popularized by local tourism developers in the early 20th century, including F.E. Hemphill and Captain Dave Edwards, who operated "glass-bottom boats" (including the Rainbow Queen) to showcase the underwater spectrum. Today, the river remains a protected state park, celebrated for its unique clarity and the vibrant, multi-colored aquatic life that gave it its namesake over a century ago.