Abstract. Measurement of intertidal rock assemblages was investigated as a potential biological indicator to provide a quantitative estimate of the impact of urbanised catchment discharge on the estuaries of Sydney, Australia, from 1995 to 1999. Based on the presence and characteristics of adjacent human activities, sampling locations were categorised as:Bush; Urban; Urban with Sewer Overflows; and Industry with Sewer Overflows. In Sydney Harbour, variation in assemblage structure was measured between most impact categories, however differences between impact categories were not consistent for each year.Nevertheless, in years of above average rainfall (1998-99), reference assemblages adjacent to national parks and distant from urbanisation were different to all other putatively impacted assemblages. Variability within assemblages was least at reference locations in each year and greatest at locations adjacent to stormwater canals and sewer overflows, particularly in 1998-1999. Variation in assemblage structure in Sydney estuaries was most strongly correlated with chlorophyll-a concentrations. Univariate analysis also identified highly significant differences for a number of factors, however, interactions between year, impact categories and location for numerous analyses, confounded the differentiation between impact categories. The results suggest that intertidal rock assemblages in Sydney Harbour and surrounding estuaries appear to be responding to the quality and quantity of discharge from urbanised catchments and, furthermore, that assemblages are more suitable than individual taxa to indicate the difference between Bush and anthropogenically disturbed estuarine locations.1 This is the version of the manuscript that was accepted for publication in Environmental Monitoring and Assessment (2005) 107: 375-398.