Manatees are an endangered species, and their population numbers have not been estimated in Panamian wetlands. Traditional monitoring methodologies using aerial surveys and visual sighting are ineffective for such turbid environments. We did a nine-month passive-acoustic survey using a Kayak with a stereo hydrophone array to detect and locate west Indian manatees in San San Pond Sak and Changuinola rivers in Panama. Twice a day transects with a total covering of 1700 km resulted 110 localizations and the recording of 1339 manatee vocalizations. Individual counting and the identification of biologically relevant sites is possible based on passive acoustics. Only a 2% of the acoustic detections were accompanied by clear sightings, indicating that visual census methodologies are ineffective in turbid environments and drastically underestimate manatee populations. We recommend this low-cost methodology to estimate manatee population more reliably in previously unsurveyed areas.