Globally, freshwater mussels are one of the most endangered taxa due to pollution, nutrient loading, habitat fragmentation, and species introduction attributable to anthropogenic activities. New Zealand freshwater mussels (kākahi) are ecological engineers and integral species in freshwater ecosystems. However, kākahi populations are expected to decline 70% by 2024 in part due to their unique reproductive cycle involving an obligatory phoretic relationship with declining native fish. Kākahi distribution and abundance throughout New Zealand is poorly understood due to time-consuming surveying techniques of concealed and morphologically cryptic species. A rapid and reliable method is required for the detection and identification of these ‘Threatened’ kākahi populations for conservation and management. Therefore, this study aimed to i) validate an environmental DNA (eDNA) based detection method for New Zealand freshwater mussels using digital PCR (dPCR); ii) determine the most appropriate sampling season for kākahi eDNA; and iii) determine whether eDNA could be used to detect effects of fish barriers on kākahi distribution. In vivo trials determined that filtration of field samples within 24 hours of collection minimised eDNA degradation and that prefiltration effectively removed inhibitory detritus and glochidia. The lowest concentration of eDNA which could accurately be detected to infer abundance (≥3.2 copies/µL) or presence (0.32-3.19 copies/µL) of kākahi eDNA was determined. Duplicate field samples were collected from the Waingaro River and Kahuhuru Stream at sites downstream of fish barriers and upstream of low-flow or all-flow barriers in December, May, and August to investigate spatial and temporal variation in eDNA concentrations. As hypothesised, December was the most effective month to sample, yielding the highest eDNA concentrations due to reduced dilution and heightened water temperatures. Based on eDNA, kākahi species distribution did not appear correlated with fish barriers, but all-flow barriers likely impeded fish host movement to significantly reduce the total kākahi eDNA concentrations found upstream. eDNA detection can be used by regional councils to effectively infer presence/absence of kākahi populations and direct further conventional surveying efforts to the most impactful locations. This method allows rapid determination of distribution and densities at a national scale to aid conservation management of this taonga (treasured) species.