Passive acoustic monitoring is gaining popularity in ecology as a practical and non‐invasive approach to surveying ecosystems. This technique is increasingly being used to monitor terrestrial systems, particularly bird populations, given that it can help to track temporal dynamics of populations and ecosystem health without the need for expensive resampling. We suggest that underwater acoustic monitoring presents a viable, non‐invasive, and largely unexplored approach to monitoring freshwater ecosystems, yielding information about three key ecological elements of aquatic environments – (1) fishes, (2) macroinvertebrates, and (3) physicochemical processes – as well as providing data on anthropogenic noise levels. We survey the literature on this approach, which is substantial but scattered across disciplines, and call for more cross‐disciplinary work on recording and analysis techniques. We also discuss technical issues and knowledge gaps, including background noise, spatiotemporal variation, and the need for centralized reference collection repositories. These challenges need to be overcome before the full potential of passive acoustics in dynamic detection of biophysical processes can be realized and used to inform conservation practitioners and managers.

Ecoacoustic methods are increasingly used to monitor the state of populations and ecosystems. In freshwater environments, they present the clear advantages of being non‐invasive, reducing bias, and providing continuous observations instead of only limited sampling snapshots in time. However, similar to standard bioassessment methods, temporal variation and choice of indicators can greatly influence ecoacoustic assessments, highlighting the importance of sampling and analysis design. In this study, we quantified diurnal variation in underwater sound and its effect on sampling regimes for two waterholes in the Einasleigh River, Northern Australia. Recording continuously for 6 days, and subsampling 5 s every 10 min, we found 22 distinct sounds that were emitted by fish, Hemiptera and Coleoptera as well as another 22 of abiotic or unknown origin. Through rarefaction analyses, we found that subsampling the data to 60% of the recorded sound events resulted in capture of most of the 44 identified sound types. Temporal heterogeneity—patchy sound events through time—needs to be considered when maximising detected sound events. Reducing the sampling interval from every 10 min to half‐hourly or hourly had a much greater effect on capturing all sound types compared to the number of days recorded or the length of the recording. Overall, only 10–20% of the sound events need to be annotated for most sound types to be described; for example, restricting analysis of the days recorded to only three and the recording interval to 0.5–1 s. Acoustic indices were dominated by three main event types—a diurnally flowing creek, a nocturnal chorus of Hemiptera, as well as a dawn chorus of terapontid fishes. We conclude with two key messages: First, a select group of informative signals can be monitored using very simple methods—namely, converting an audio stream into indices using freely available software. Second, however, to detect less acoustically dominant sound events, manual annotation or single call processing will still be needed. While these findings are encouraging, similar analysis will need to be conducted within other freshwater ecosystems before general conclusions about optimal sampling regimes can be drawn.

Biodiversity in freshwater habitats is decreasing faster than in any other type of environment, mostly as a result of human activities. Monitoring these losses can help guide mitigation efforts. In most studies, sampling strategies predominantly rely on collecting animal and vegetal specimens. Although these techniques produce valuable data, they are invasive, time‐consuming and typically permit only limited spatial and temporal replication. There is need for the development of complementary methods. As observed in other ecosystems, freshwater environments host animals that emit sounds, either to communicate or as a by‐product of their activity. The main freshwater soniferous groups are amphibians, fish, and macroinvertebrates (mainly Coleoptera and Hemiptera, but also some Decapoda, Odonata, and Trichoptera). Biophysical processes such as flow or sediment transport also produce sounds, as well as human activities within aquatic ecosystems. Such animals and processes can be recorded, remotely and autonomously, and provide information on local diversity and ecosystem health. Passive acoustic monitoring (PAM) is an emerging method already deployed in terrestrial environments that uses sounds to survey environments. Key advantages of PAM are its non‐invasive nature, as well as its ability to record autonomously and over long timescales. All these research topics are the main aims of ecoacoustics, a new scientific discipline investigating the ecological role of sounds. In this paper, we review the sources of sounds present in freshwater environments. We then underline areas of research in which PAM may be helpful emphasising the role of PAM for the development of ecoacoustics. Finally, we present methods used to record and analyse sounds in those environments. Passive acoustics represents a potentially revolutionary development in freshwater ecology, enabling continuous monitoring of dynamic bio‐physical processes to inform conservation practitioners and managers.