Autonomous acoustic telemetry monitoring systems have been deployed in aquatic ecosystems around the globe – from under ice sheets in the Arctic to coral reefs in Australia – to track animals. With tens of thousands of tagged aquatic animals from a range of taxa, vast amounts of data have been generated. As data accumulate, it is useful to reflect on how this information has advanced our understanding of aquatic animals and improved management and conservation. Here we identify knowledge gaps and discuss opportunities to advance aquatic animal science and management using acoustic telemetry monitoring. Current technological and analytical shortfalls still need to be addressed to fully realize the potential of acoustic monitoring. Future interdisciplinary research that relies on transmitter-borne sensors and emphasizes hypothesis testing will amplify the benefits of this technology.