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Groundwater ecosystems within the Greater Wellington region are not currently routinely monitored, creating a significant gap in our understanding of their baseline characteristics and ecological health. This lack of knowledge hampers their practical use as reliable indicators of environmental stress. To address this, the Greater Wellington Regional Council and the New Zealand Institute for Public Health and Forensic Science (PHF Science) collaborated on a pilot study within the Hutt aquifer system. The study aimed to obtain a preliminary assessment of groundwater macrofauna, meiofauna and microbial communities (collectively stygofauna groundwater biodiversity) and to refine cost-effective sampling techniques for more routine and widespread monitoring.