Invasive species threaten biodiversity in Aotearoa New Zealand. In wetlands − significant sites that provide an array of ecosystem and cultural services but represent <10% of their original extent − invasive species can affect hydrological function, nutrient regimes and overall ecological functionality. Environmental DNA (eDNA) has emerged as a valuable biomonitoring technique for cataloguing biodiversity and detecting biological incursions, but little is known about how biodiversity varies in wetlands over fine and broad spatial scales. Here, we examined the publicly available eDNA database of Wilderlab New Zealand, retrieving data from 26 sites across the country to characterise taxonomic diversity patterns, including the extent of exotic and non-exotic (native and endemic) species. We found significant spatial variation in biodiversity–even among neighbouring sites–and a pattern whereby all sites had ≥50% exotic species in their total species tally. Our results provide new information on the current state of wetland biodiversity in Aotearoa New Zealand and highlight the value of eDNA databases for generating new insights from publicly shared data. They also emphasise an urgent need for greater resource allocation to conservation and restoration initiatives in Aotearoa New Zealand that will ensure the persistence of treasured native and endemic wetland species.