AbstractFor many species at risk, monitoring challenges related to low visual detectability and elusive behavior limit the use of traditional visual surveys to collect critical information, hindering the development of sound conservation strategies. Passive acoustics can cost‐effectively acquire terrestrial and underwater long‐term data. However, to extract valuable information from large datasets, automatic methods need to be developed, tested and applied. Combining passive acoustics with deep learning models, we developed a method to monitor the secretive Amazonian manatee over two consecutive flooded seasons in the Brazilian Amazon floodplains. Subsequently, we investigated the vocal behavior parameters based on vocalization frequencies and temporal characteristics in the context of habitat use. A Convolutional Neural Network model successfully detected Amazonian manatee vocalizations with a 0.98 average precision on training data. Similar classification performance in terms of precision (range: 0.83–1.00) and recall (range: 0.97–1.00) was achieved for each year. Using this model, we evaluated manatee acoustic presence over a total of 226 days comprising recording periods in 2021 and 2022. Manatee vocalizations were consistently detected during both years, reaching 94% daily temporal occurrence in 2021, and up to 11 h a day with detections during peak presence. Manatee calls were characterized by a high emphasized frequency and high repetition rate, being mostly produced in rapid sequences. This vocal behavior strongly indicates an exchange between females and their calves. Combining passive acoustic monitoring with deep learning models, and extending temporal monitoring and increasing species detectability, we demonstrated that the approach can be used to identify manatee core habitats according to seasonality. The combined method represents a reliable, cost‐effective, scalable ecological monitoring technique that can be integrated into long‐term, standardized survey protocols of aquatic species. It can considerably benefit the monitoring of inaccessible regions, such as the Amazonian freshwater systems, which are facing immediate threats from increased hydropower construction.