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Long term-monitoring of an intertidal sandflat in Durban Bay, South Africa, indicated a major regional transformation in macrofauna between 1994 and 2002. This sandflat, known as Little Lagoon, was composed of muddy sand in 1994, but became more sandy by 2002. This change coincided with the establishment of dense beds of the burrowing sandprawn Callianassa kraussi, and a major decline in bivalve richness and density. In 1994, bottom-feeding fish dominated the ichthyofauna, with bivalve siphons dominating their diets. In 2002, however, the fish community was dominated by zooplanktivorous fish, and bivalve siphons were absent in the stomachs of benthic fish. We hypothesised that increases in C. kraussi density between 1994 and 2002 contributed to these changes in macrofauna. To test this hypothesis, macrofauna was compared between areas of high and low C. kraussi density in Little Lagoon in 2002, to determine whether pattern differences between these areas mirrored those between 1994 and 2002. Both investigations showed that C. kraussi was negatively associated with abundances of suspension feeders, deposit feeders and surface grazers, but not with burrowing infauna abundance. Densities of bivalves in particular, were significantly reduced in areas heavily bioturbated by C. kraussi. These trends have since been demonstrated experimentally, and support our hypothesis that an increase in C. kraussi density contributed to these changes to macrofauna. This long-term study also highlights the 'ecosystem-engineering' role of C. kraussi, and suggests that its effects ripple through higher trophic levels by reducing the abundance of food items.