Mudflats in estuarine and coastal areas are of high ecological and socio-economic importance, underpinning food-webs, supporting fisheries, and providing shoreline protection. Central to these functions of mudflats are microphytobenthos (MPB) -- microscopic photosynthesizers at the base of the food web. Local and global environmental change has the potential to modify the productivity and community composition of MPB, both directly and also indirectly, by altering the identity and density of macrofauna – which consume MPB and disturb sediments. Through controlled aquarium experiments, this study investigated the independent and interactive effects of two macrobenthic species—Pyrazus ebeninus, a deposit feeder, and Trypaea australiensis, a burrower—on colonization of MPB, under scenarios of (no, low or high) nutrient enrichment. Effects of macrofauna on MPB were strongest at the low level of nutrient enrichment, with a lower chlorophyll a to phaeopigment ratio in the treatment with only Pyrazus than the other treatments (no animals, or Trypaea with or without Pyrazus), indicating species-specific effects of macrofauna. The results highlight the importance of macrofauna in shaping MPB, and the sensitivity of these interactions to environmental change. Disentangling these relationships will be important for estuarine ecosystem management in a changing environment.