Biological monitoring has a long history in freshwaters, where much of the pioneering work in this field was developed over a 100 years ago—but few of the traditional monitoring tools provide the global perspective on biodiversity loss and its consequences for ecosystem functioning that are now needed. Rather than forcing existing monitoring paradigms to respond to questions they were never originally designed to address, we need to take a step back and assess the prospects for novel approaches that could be developed and adopted in the future. To resolve some of the issues with indicators currently used to inform policymakers, we highlight new biological monitoring tools that are being used, or could be developed in the near future, which (1) consider less-studied taxonomic groups, (2) are standardised across regions to allow global comparisons, and (3) measure change over multiple time points. The new tools we suggest make use of some of the key technological and logistical advances seen in recent years—including remote sensing, molecular tools, and local-to-global citizen science networks. We recommend that these new indicators should be considered in future assessments of freshwater ecosystem health and contribute to the evidence base for global to regional (and national) assessments of biodiversity and ecosystem services: for example, within the emerging framework of the Intergovernmental Platform on Biodiversity and Ecosystem Services.