High water temperatures and low water levels provide the perfect breeding ground for this rare amoeba, called Naegleria fowleri, officials said. They warned the public "to be wary when swimming, jumping or diving in freshwater" with these conditions.
Zachary's family told CNN affiliate WBBH-TV that the boy was kneeboarding with friends in a water-filled ditch by his house on August 3. He slept the entire next day.
Zachary is an active seventh-grader, his family said, so sleeping that much was unusual. His mother took him to the hospital immediately. He had brain surgery, and doctors diagnosed him with primary amoebic meningoencephalitis, according to WBBH. The family said he is currently in the intensive care unit at the Miami Children's Hospital.
The Centers for Disease Control and Prevention said it has been in touch with Zachary's doctors and has released the same experimental anti-amoeba drug used to treat 12-year-old Kali Hardig recently in Arkansas. The Arkansas girl is only the third person in the last 50 years to survive this deadly parasite.
Kali was infected with the same parasite a couple of weeks ago and was at Arkansas Children's Hospital in Little Rock.
The cases are nearly always deadly, but Kali's condition is giving the Reyna family some hope.
"We continue to be amazed by Kali's progress," her family said in a statement Thursday. "Today she's able to sit up on her own, write some words on a white board and stand with assistance for very brief stretches. She's even able to throw and catch a ball with her therapists. We are grateful for the continued prayers from Kali's supporters, which no doubt drive her recovery."
Her attending physician, Dr. Vikki Stefans at Arkansas Children's Hospital's Progressive Rehab Unit, said in a statement Thursday: "Kali's progress is definitely a credit to her wonderful family and support system," Stefans said. "There is no longer a question of whether she'll survive and do well, but just how well."
Zachary's family is hoping he becomes survivor No. 4.
"He's strong," his brother, Brandon Villarreal, told WBBH. "He's really, really strong."
Getting Naegleria fowleri is extremely rare; between 2001 and 2010, there were only 32 reported cases in the United States, according to the CDC. Most of the cases have been in the Southeast.
Naegleria fowleri is found in hot springs and warm freshwater, most often in the Southeastern United States. The amoeba enters the body through the nose and travels to the brain. There is no danger of infection from drinking contaminated water, the CDC said.
"This infection is one of the most severe infections that we know of," Dr. Dirk Haselow of the Arkansas Department of Health told CNN affiliate WMC-TV about Kali's case. "Ninety-nine percent of people who get it die."
Dr. Sanjiv Pasala, one of Kali's attending physicians, said doctors immediately started treating the girl with Impavido, an experimental anti-amoeba drug they received directly from the CDC. They also reduced the girl's feverish body temperature to 93 degrees. Doctors have used that technique in some brain injury cases as a way to preserve undamaged brain tissue.
Several weeks ago, doctors checked the girl's cerebral spinal fluid and could not find any presence of the amoeba.
Willow Springs Water Park in Little Rock is the most likely source of Kali's infection, the Arkansas Department of Health said. Another case of the same parasite was reported in 2010 and was possibly linked to Willow Springs, a three-acre sand-bottom, spring-fed lake.
"Based on the occurrence of two cases of this rare infection in association with the same body of water and the unique features of the park, the ADH has asked the owner of Willow Springs to voluntarily close the water park to ensure the health and safety of the public," the health department said.
Willow Springs' website says its water is pH-balanced, chemically treated, chlorinated and routinely monitored by the health department.
The first symptoms of primary amoebic meningoencephalitis appear one to seven days after infection, including headache, fever, nausea, vomiting and a stiff neck, according to the CDC.
"Later symptoms include confusion, lack of attention to people and surroundings, loss of balance, seizures and hallucinations," the agency website says. "After the start of symptoms, the disease progresses rapidly and usually causes death within one to 12 days."
Here are some tips from the CDC to help lower the risk of infection:
• Avoid swimming in freshwater when the water temperature is high and the water level is low.
• Hold your nose shut or use nose clips.
• Avoid stirring up the sediment while wading in shallow, warm freshwater areas.
• If you are irrigating, flushing or rinsing your sinuses (for example, by using a neti pot), use water that has been distilled or sterilized.
CNN's John Bonifield and Caleb Hellerman contributed to this report.