This article describes the relationship between 10 selected properties of the sediments (chlorophyll a and b, colloidal and total carbohydrate, water concentration, sediment type, organic matter, erosion threshold and erosion rate) and meio- and macrofauna within and among three different habitats in an urbanized intertidal mudflat/mangrove forest in Tambourine Bay, Sydney Harbour, Australia. Many of the biogeochemical variables were significantly different among habitats, often grading from mudflat to mangrove canopy. In contrast to previous studies, patterns of distribution of macrofauna among habitats were weak. For the meiofauna, only copepods showed any significant difference among habitats, with the greatest numbers in the open mudflat habitat and least under the mangrove canopy. There was a gradient in fauna among the habitats; overall macrofauna abundances were greatest under the mangrove canopy and least on the mudflat, while meiofauna abundance was greatest in the pneumatophore habitat and least under the canopy. Correlations between fauna and properties of sediment were generally weak. When the habitats were analysed separately, some correlations were strengthened but relationships were inconsistent. Thus, while some taxa vary significantly among habitats there was not a strong relationship between biogeochemical properties and either macro- or meiofauna. This suggests that localised factors other than the measured properties of the sediments are driving patterns in fauna at these small scales, which requires further investigation to be unravelled.