During the first trimester of 2020, the Ministry of Health of Costa Rica reported the first three cases of primary amebic meningoencephalitis (PAM). In two cases, laboratory personnel of the hospitals preliminarily identified amoeboid forms in cerebrospinal fluid (CSF) samples. For the molecular confirmation of species, CSF samples were sent to our laboratory. We carried out microscopic analyses and exflagellation assays. Besides, samples were cultured in 2% casein hydrolysate medium and in non-nutrient agar plates supplemented with Escherichia coli. Finally, PCR and sequencing were employed for the molecular diagnosis and species identification. In all cases, the presence of Naegleria fowleri was confirmed. An environmental investigation to identify the possible infection sources was also performed. Water samples from hot springs and groundwater from an artisan well were collected and after filtration and culture in non-nutrient agar plates supplemented with E. coli, thermotolerance and exflagellation assays were carried out. For the positive samples, PCR and sequencing were performed, confirming the presence of N. fowleri in several water samples. The report of these cases and the possible association with hot springs has had a significant impact on the population and health authorities of Costa Rica.