Context Understanding how ecosystems function to deliver services is essential if we are to limit the impacts off human activities. Aim We hypothesised that increased densities of whelk, Pyrazus ebeninus, and crab, Macrophthalmus setosus, up to four times (given their large body-size and ecological roles, e.g. consuming deposits and disturbing sediments) would affect the macrofaunal community and how it functions in a south-eastern Queensland mudflat. Method The biota and physical environment of the field-deployed cages (three density treatments, caged and control plots) were sampled up to 90 days. Results After 90 days, the redox discontinuity layer was deeper and sediment organic matter was higher in all density treatments. This is consistent with enhanced burrowing, surface disturbance, mucus and pellet production. However, no significant changes in the taxonomic composition of the unmanipulated portion of the macrofaunal resident assemblage were observed. Conclusion Whereas some communities change structurally when perturbated and then revert, this community remained in the new manipulated configuration for at least 90 days. Implications Limited understanding of the ecological relationships in these systems, such as the processes operating to support this large increase in deposit-feeding biomass constrains evidence-based management. These systems may be able to, at least temporally, support enhanced biomasses and levels of ecosystem services.