Bivalves are ecosystem engineers, and their effective management relies on a full understanding of the mechanisms that influence population dynamics. Juvenile tuaki (New Zealand cockle) Austrovenus stutchburyi, a numerically dominant and ecologically important bivalve in New Zealand estuaries, were found at higher densities when surrounded by high densities of large adults within Waitati Inlet, in southern New Zealand. Consequently, we hypothesised that adults provided a refuge from predation for juveniles, resulting in higher juvenile survival and retention in dense beds. The observed pattern was consistent with post-settlement Allee effects, where declines in density and truncated size distributions may have resulted in unsuccessful recruitment if a density threshold was reached. Field experiments were undertaken in 2020 and 2021 to test the potential sheltering effect of adults on retention and survival of juveniles, with and without the addition of organic loading of sediments. Presence of adults had significant effects on juvenile retention and interaction with organic loading in 2020, but not in 2021. To isolate the effects of adult presence on predation of juveniles, a series of laboratory experiments were carried out using the predatory crab Ovalipes catharus. Juvenile survivorship from crab predation was enhanced in the presence of large adults, consistent with the hypothesised sheltering effect. Further, predation rates increased significantly from winter to summer, which correlated with increasing water temperatures and the breeding and moult cycle of crabs. These findings across surveys, field and laboratory manipulations have significant implications for effective fisheries management and restoration of bed-forming bivalves.