Biodiversity in freshwater habitats is decreasing faster than in any other environment, mostly due to human activities. Monitoring these losses can help guide mitigation efforts. In most comparative or focal studies, sampling strategies predominantly rely on collecting animal and vegetal specimens. Although these techniques have produced valuable data, they are invasive, time-consuming, and typically have limited spatial and temporal replication. There is therefore a need for the development of complementary methods. As with other ecosystems and landscapes, freshwater environments host animals producing sounds, either to communicate or as a byproduct of their life activity. Animals and processes can be recorded, remotely, by unattended equipment and provide global information on local diversity and ecosystem health. We review practical examples of progress in experimentally addressing six main challenges that freshwater ecoacoustic monitoring faces: (1) associating each sound to its emitter, (2) estimating intra-specific sound variations, (3) evaluating diurnal variation, (4) modeling sound propagation, (5) deriving links between ecological condition and sounds, and (6) developing a repository for freshwater sounds. Passive acoustics represents a potentially revolutionary development in freshwater ecology, enabling dynamic monitoring of biophysical processes to inform conservation practitioners and managers.