Groundwater organisms provide ecosystem services for the quality of ground and surface waters (Mammola et al., 2019). These microorganisms and invertebrates can transform and degrade contaminants or maintain hydraulic conductivity. However, biodiversity assessments for aquifers are generally not available. To monitor and assess biodiversity levels in the aquifers and other water bodies, eDNA will be used to ensure the possibility of studying rare and/or elusive species that serve as bio-indicators of water and soil quality.