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Spatial patterns in the number of species, number of individual animals and community composition of the benthos of the Hawkesbury Estuary, N.S.W., are described and related to physicochemical factors. Replicate grabs were taken from deep and shallow sites located on transects across the estuary for each of five times at intervals of 3 months. The number of species and number of individuals always differed significantly along the estuary but the pattern of difference varied with both depth and time. Although a monotonic decline in the number of species along the estuary never occurred, the two most- seaward transects usually supported the most species and the three furthest-upstream transects the least. The number of species was usually more highly correlated with salinity than with sedimentary variables but salinity correlations were not always significant. The number of individuals was not related to any abiotic variable in a consistent way. Significant depth-related differences occurred only for the number of individuals although the pattern of difference varied among both transects and times. Sediment-associated differences also varied with transect and time. Where consistent differences occurred, highest species numbers were sometimes associated with sand and sometimes with coherent clay. Consequently the species-sediment relationship is not always a simple linear function of grain size and different aspects of sediment structure may be influential. Sediments with greater habitat heterogeneity sometimes supported more species and sometimes fewer species than more uniform sediments. Classification and ordination analyses revealed major patterns in community composition that were most closely related to salinity and minor patterns related to sediment grade. Community changes did not always correspond with physicochemical changes and hence the latter were not always good predictors of biological variables.