We assessed the usefulness of environmental DNA (eDNA) for monitoring the introduced pest fish Gambusia affinis by filtering water samples from streams in the Nelson and Tasman regions, South Island, New Zealand, known to contain G. affinis, and from streams where G. affinis were absent. We used the Smith Root DNA sampler backpack with two types of filters (1.2 and 5 µm pores), to filter water and capture eDNA, and used quantitative polymerase chain reactions (qPCR), and digital droplet PCR (ddPCR) to measure the amount of G. affinis DNA collected by the two filter sizes. We also used high throughput (Illumina MiSeq) sequencing (HTS) to detect G. affinis. Results from the two PCR methods and the high throughput sequencing were compared to hand net counts of G. affinis. We found that all three methods were equally successful at detecting G. affinis when four replicates were taken from each site, but that sensitivity over all replicates was ddPCR > qPCR > HTS. We conclude that the use of environmental DNA to detect the presence of G. affinis is a useful tool to assist in mapping the distribution of G. affinis and will aid in the control of this invasive species.