Intertidal rock pools support diverse assemblages. While there is much research on the importance of rock pools in supporting mobile diversity on rocky shores, there is limited knowledge regarding the role of physical features (microhabitats) within these habitats. Understanding the features of pools that support diversity is crucial to conserve and potentially mimic these important intertidal habitats in restoration projects. Here, we classified and quantified the types of physical features, hereafter “microhabitats” (overhangs and pits), within rock pools at different locations in and around a highly urbanised estuary, Sydney Harbour, Australia. The use of different microhabitats within rock pools by mobile macro-invertebrates was also examined in one location. We surveyed natural rock pools in summer (2 times) and winter (2 times) at seven sites: two sites from each of the inner and outer zones of Sydney Harbour, and three sites along the open coast of Sydney. We found that the type and size of microhabitats within pools decreased from the coastal towards inner harbour sites. Along the open coast, the richness of mobile taxa increased in rock pools with overhangs or pits. Only rock pools with overhangs had increased mobile abundances, likely driven by the gastropod Nerita melanotragus. Several species occurred in greater frequency in pools with overhangs. There was no effect of pits on abundances. This survey suggests that some microhabitats may play an important role in the diversity and abundance of mobile macro-invertebrates in rock pools. A detailed understanding of the local and regional scales of microhabitats should be used to inform eco-engineering of intertidal foreshores.