Determining interactions between biological and physical structure of intertidal sediments and their relationships to ecological functioning is vital for improving our understanding of these complex habitats. If spatial and/or temporal variations in the benthos are related to properties of the sediment, one can infer that sediments should vary and change at similar scales to the benthos. The mangrove forests of Sydney Harbour, Australia consist of distinct subhabitats (termed MH1-3, representing a change from open mudflat to canopied mangrove forest), which might affect benthos and, independently, properties of the sediment. This study tests the model that the benthos and sediment would respond to environmental differences between MH1–3 similarly in different locations and thus show consistent patterns of difference among habitats. Although general patterns of sediment properties and benthos were relatively similar, detailed patterns varied among locations. The relative importance of the different sedimentary properties varied in unpredictable ways among habitats in the different locations. Out of all the variables, only total carbohydrate was consistently important in driving differences among habitats in all three locations, but only between MH1 and MH2. That there were no other strong consistent differences between the different microhabitats in terms of the measured properties of the sediments indicates that there is more driving these patterns than a simple relationship to different habitat formed by mangrove forests and/or feedbacks between sediment properties and benthos. With respect to the benthic assemblage, in all bays MH1 and MH3 were the most different. The benthos showed stronger patterns relating to the different subhabitats than did the sediment, suggesting that there are important differences affecting these habitats that were not revealed by our suite of biogeochemical measurements of the sediment.