This is the time of year when there is an uptick in cases.
Health officials usually record about two to three cases in a given year -- 1980 was the highest with eight deaths.
And most of the time, they occur in children and teenagers.
"These are rare infections, but super tragic for families," said Jonathan Yoder, the waterborne disease and outbreak surveillance coordinator at the Centers for Disease Control and Prevention.
"We don't want to minimize how hard it is for families."
The amoeba, called Naegleria fowleri, is the only type that infects humans and is more than 95% lethal.
The first death in 2011 occurred in June in Louisiana, according to the CDC.
The most recent involved a 16-year-old girl who died Saturday after becoming infected by an amoeba in Brevard County, Florida, according to CNN's affiliate WFTV.
The amoeba could have entered the teen's body as the teen swam in a nearby river.
The central Florida station reported that the teenager had suffered fever, nausea and headaches.
A spinal tap showed that Naegleria fowleri was present in her spinal fluids.
In another case, the Virginia Department of Health confirmed Friday that a child from central Virginia died from primary amoebic meningoencephalitis, which is caused by the amoeba.
The Richmond Times Dispatch said the child was a 9-year-old boy from Henrico County.
The child died within the last few weeks, said Dr. Keri Hall, the state's director of epidemiology.
She declined to share other details. Virginia's last confirmed case was in 1969.
Amoeba infections in humans are extremely rare.
The CDC found 32 reported cases in 10 years -- compared with 36,000 drowning deaths from 1996 to 2005.