The world’s coastlines have become heavily modified over the last century, with the adjacent natural habitats declining in biodiversity and health under increasing pressure from urbanisation. In this study we assessed the structure and biological traits of macrofaunal assemblages from 24 south-east Queensland mudflats in order to determine whether ecological functioning (e.g. primary production, nutrient cycling) and the delivery of ecosystem services was affected by urbanisation. This work represents the most comprehensive assessment of mudflat assemblages in the region to date. The mudflats contained 50 macrofaunal taxa and so were comparable to other local intertidal systems. Summer assemblages contained more species, more individuals and had differing taxonomic composition. When indexed as a proportion of subcatchment area, urbanisation did not correspond to a clear impact on macrofaunal composition; rather, the nature of the industry or activity was critical. Mudflats from subcatchments with industries producing organic wastes significantly differed from subcatchments with <1.3% cover of these industries. Functioning was conserved in mudflats experiencing current levels of enrichment, but this may decline with growing pressure from human populations. The results of this study illustrate that large-scale spatial data, such as from satellites, can be used to detect the cumulative effects of urbanisation when the pressures are highly resolved.