This month, the infection - Naegleria fowleri - killed a 16-year-old Florida girl, who became sick after swimming, and a 9-year-old Virginia boy, who died a week after he went to a fishing day camp.
The third case was in Louisiana. A young man died in June, and his death was traced to the tap water he used in a device called a neti pot - a small teapot-shaped container used to rinse out the nose and sinuses with salt water to relieve allergies, colds and sinus trouble.
Health officials later found the amoeba in the home's water system. The problem was confined to the house; it wasn't found in city water samples, said Dr. Raoult Ratard, Louisiana's state epidemiologist.
The illness is extremely rare. About 120 U.S. cases - almost all of them deaths - have been reported since the amoeba was identified in the early 1960s, according to the Centers for Disease Control and Prevention.
About three deaths are reported each year, on average, and officials say there are no signs that cases are increasing.
Naegleria fowleri is found in warm lakes and rivers during the hot summer months, mostly in the South.
The Associated Press contributed to this report.