According to the the U.S. Army Corps of Engineers, tests taken in January show that Lake Huron and Lake Michigan were 68 cm below their long term average. Since January last year, they've dropped an alarming 43 cm.
The other three Great Lakes, Superior, Erie and Ontario, are also well below average, raising concerns about heavy economic losses.
Low water levels can also cause significant damage to fish spawning areas.
Scientists blame drought and other natural forces for the below average levels. Dredging of rivers that drain from the lakes have also contributed to the level drops.
Officials warn that water levels could continue to get lower due in part to lower than usual snow and rainfall.
With files from The Associated Press