We review the progress made in building capacity and consensus around field and laboratory methods during the course of the DNAqua-net programme, including short-term scientific missions, training courses, workshops and ring tests. We highlight the challenge of methodological standardisation, where in some cases the same written protocol employed by different laboratories may not always give the same results, but in other cases almost identical results can be obtained using different methodological workflows. As the field of DNA-based biomonitoring moves increasingly into practical application, we consider how end-users can best ensure quality and consistency of results, while also enabling continued technical innovation, which will continue to move the field forwards. We also reflect on the benefits of multi-stakeholder forums such as DNAqua-net for bridging the research-policy gap and accelerating the application and impact of research. Finally, we introduce a major output from the working group: A Practical Guide to DNA-based Methods for Biodiversity Assessment, which synthesises current knowledge to help end-users or those new to the field to understand the methodological choices that have to be made, and the trade-offs implicit in those choices.