Rock pools provide a range of ecological niches that can support diverse assemblages on rocky shores. As intertidal shores are increasingly lost to developments, understanding the drivers of diversity in rock pools is important for the conservation and construction of these key habitats. In this study we investigated relationships between physical characteristics of rock pools and their biota in an urban estuary. We sampled the biota every 6 weeks for 1 year at sites in the inner and outer zones of Sydney Harbour. In the well-flushed and exposed outer zone, sessile and mobile taxa richness was positively related to rock pool width, whereas only mobile taxa richness was related to depth and volume. In the more urbanised and less exposed inner zone, mobile taxa richness was positively related to rock pool width and volume. In both zones, sessile taxa richness decreased with increasing height on shore. Our results suggest that the biodiversity of intertidal rock pools varies depending on their position in Sydney Harbour and the available species pool. Therefore, restoration efforts should consider rock pool size parameters and local environmental conditions, including location, so designs can be optimised to maximise species diversity in these pools.