We tested the ability of pollution induced community tolerance (PICT) to detect the effects of chronic metal pollution on estuarine sediment microbial communities, along a gradient spanning two orders of magnitude in metal concentrations. In tandem, we investigated the associated microbial community structure using terminal restriction fragment length polymorphism (T-RFLP). Tolerance of microbes to Cu, measured as IC50 (inhibitory concentration 50%), was strongly correlated with pore water Cu concentration (r2 = 0.842). No strong correlation existed for other metals tested, highlighting the ability of PICT to identify the pollutant causing a toxic effect. There was no correlation between microbial community structure and community tolerance to metals tested, but analysis of community structure did provide some information on reasons for observed PICT response. PICT methodology used here provided a greater strength and consistency of association with pollutant concentration compared to microbial community structure and can be recommended as a sensitive indicator of metal pollution on estuarine sediment microbial communities.