Ecosystem-based management (EBM) requires more extensive information than single-species management. Active underwater acoustic methods provide a means of collecting a wealth of ecosystem information with high space-time resolution. Worldwide fisheries institutes and agencies are carrying out regular acoustic surveys covering many marine shelf ecosystems, but these data are underutilized. In addition, more and more acoustic data collected by vessels of opportunity are becoming available. To encourage their use for EBM, we provide a brief introduction to acoustic and complementary data collection methods in the water column, and review current and potential contributions to monitoring population abundance and biomass, spatial distributions, and predator-prey relationships. Further development of acoustics-derived indicators is needed. We review and propose indicators for assessing and monitoring zooplankton, population dynamics of fish and other nekton, and changes in diversity and food-web functioning. Acoustic methods have the potential to make a strong contribution to EBM. Evaluation of new indicators and suitable reference points in different ecosystems are the current challenges.