One lake was so large that a mile-wide crater was left behind after it was drained in the span of a few weeks. Another sub-glacial lake has been filled and emptied twice in the last two years.
The findings were published separately for each lake in the journals "Nature" and "The Cryosphere."
"The draining of the lake may be showing us that the plumbing system under the ice is changing because more water is melting from the surface and flowing into it," Howat told ABC News.
The second lake was discovered by a team from Cornell University. When mapping Greenland's ice sheet, the team learned that when the lake is drained and filled again, it creates stored heat that can change the composition of the ice.
The problem is further exacerbated by overflowing meltwater hindering the ice sheet's drainage system. This creates what researchers call "blowouts," leading to drainage.
Howat said it's possible there are more sub-glacial lakes in Greenland that have yet to be discovered.
"First, we now know that these lakes can exist, but we don't know how many lakes there are or how much water is in them," he said. "If there's a lot, then draining of lakes could be another way that melt of the ice sheet contributes to [a rise in] sea level."