Abstract Relationships between ecological structure, functions and properties of sediments in intertidal mangrove forests and mudflats are poorly understood. Studies have not yielded consistent results, due to complex interactions between biotic and abiotic components. The benthic macrofauna in mangrove forests are important contributors to ecological functions, mediating various sedimentary properties. They vary in abundance and diversity at scales from centimeters to hundreds of metres in what appears to be similar “habitat”, but properties of sediments are often not measured at such small scales, or small-scale variation is ignored as random noise. Yet, there should be relationships between scales of variation in macrofauna and bio-dependant properties of sediments. This paper describes variation in assemblages of benthic invertebrates and bio-dependant properties of sediments at a hierarchical range of spatial scales, within and among different habitats in an urbanized mangrove forest and the associated intertidal mudflats in Sydney Harbour, Australia. Measurements were made on two occasions, in replicate sites in each habitat. These were used to test hypotheses about relationships of scales of variation in the benthos and sediments. The benthos showed relatively little difference in diversity and abundances among habitats compared to variation within and between sites in each habitat. The bio-dependant properties of the sediment showed less variation at small scales and larger among-habitat variation than did the benthos. Variation in the benthos did not clearly correlate with variation in the selected bio-dependant properties of the sediments at any scales. Neither did the properties of the sediment show consistent correlations in any habitat. These data indicate that the properties and processes driving the benthos are not simply related to the properties of the sediment we measured and that there was very large variation in both benthos and bio-dependant properties within small sites. This highlights the necessity of using experimental designs that sample at a hierarchy of scales for benthic assemblages and bio-dependant properties of sediment.