The genetic material was from silver carp, one of two Asian species threatening to enter the Great Lakes, where scientists say they could out-compete native fish for food.
The water samples were among 350 collected by state and federal agencies in July and August. Officials announced earlier that 20 samples taken from Lake Erie's Sandusky Bay had tested positive for silver carp DNA.
The findings were announced Tuesday by the Michigan and Ohio natural resources departments.
They said the results raise further concerns that Asian carp may have invaded Lake Erie. But no actual fish have been found. The presence of DNA doesn't indicate how many carp might be in the lake.