Aquaculture of New Zealand’s endemic green-lipped mussel (Perna canaliculus) is an industry valued at NZ$ 336 M per annum and is ~ 80% reliant on the natural supply of wild mussel spat harvested at a single location—Te Oneroa-a-Tōhē—Ninety Mile Beach (NMB)—in northern New Zealand. Despite the economic and ecological importance of this spat supply, little is known about the population connectivity of green-lipped mussels in this region or the location of the source population(s). In this study, we used a biophysical model to simulate the two-stage dispersal process ofP. canaliculus. A combination of backward and forward tracking experiments was used to identify primary settlement areas and putative source populations. The model was then used to estimate the local connectivity, revealing two geographic regions of connectivity in northern New Zealand, with limited larval exchange between them. Although secondary dispersal can double the dispersal distance, our simulations show that spat collected at NMB originate from neighbouring mussel beds, with large contributions from beds located at Ahipara (southern end of NMB). These results provide information that may be used to help monitor and protect these important source populations to ensure the ongoing success of the New Zealand mussel aquaculture industry.