The New Zealand cockle Austrovenus stutchburyi is often found stranded on the sediment surface due to infections by echinostome trematodes. High densities of heavily-infected cockles on the sediment surface affect near-seabed hydrodynamics and sedimentation and, in turn, benthic animal community structure and diversity. In a six-month field experiment on an intertidal sandflat we manipulated the density of cockle mimics on the sediment surface, and here we show that their presence had two significant impacts on community functioning. First, the benthic primary production (in terms of chlorophyll-a content) was reduced by 8–22%. Second, their presence significantly boosted (up to 5-fold) the secondary production (in terms of biomass) of Coelenterata, Nemertea, small polychaetes, small bivalves and the gastropod Diloma subrostrata. The results hence provide a field experimental example of a parasite-mediated link between diversity and productivity.