In our most recent study, published in Scientific Reports (https://doi.org/10.1038/s41598-023-44908-8), we used participatory science and environmental DNA (eDNA) metabarcoding to investigate groundwater amphipods and to capture a broader picture of the groundwater community, including microorganisms. Combining both methods revealed co-occurring amphipod species and their correlation with overall groundwater biodiversity, enhancing our understanding of subterranean ecosystems. In conclusion, we propose two novel methods for studying groundwater organisms, which can be applied independently or, more effectively, in combination. These approaches offer valuable tools for addressing uncharted aspects of subterranean biology.