Scientists ran more than 100 computer models to see if anything else could be having an impact on Ganymede's aurora. They also repeated the seven-hour, ultraviolet Hubble observations and analyzed data for both belts of aurora.
"This gives us confidence in the measurement," Saur said.
NASA Planetary Science Division Director Jim Green called the finding "an astounding demonstration."
"They developed new approach to look inside a planetary body with a telescope," Green said.
Ganymede joins a growing list of moons in the outer solar system with subsurface water. On Wednesday, scientists reported that Saturn's moon Enceladus has hot springs beneath its icy crust. Other water-rich worlds include Jupiter moons Europa and Callisto.
Scientists estimate the ocean is 60 miles (100 km) thick, 10 times deeper than Earth's oceans, and is buried under a 95-mile (150-km) crust of mostly ice.
"It is one step further toward finding that habitable, water-rich environment in our solar system," said astronomer Heidi Hammel with the Washington-based Association of Universities for Research in Astronomy.