Mark-recapture study designs which accommodate heterogeneity in capture probabilities associated with individual animals moving between geographic sites can provide insight into mammal distributions in terrestrial and marine environments and the status and connectivity of subpopulations. Using a multistate closed robust design (MSCRD) approach, we investigated demographic parameters of Indo-Pacific bottlenose dolphin (Tursiops aduncus) subpopulations in coastal and estuarine waters of Perth, Western Australia, and the relationship between subpopulations in a metapopulation. Using year-round photo-identification surveys across multiple geographic sites, we accounted for heterogeneity of capture probability based on how individuals distribute themselves across sites and characterised the status of subpopulations based on their abundance, survival and interconnection. MSCRD models highlighted high heterogeneity in capture probabilities and demographic parameters between sites. High capture probabilities, high survival and constant abundances described a subpopulation with high site fidelity in an estuary, while low captures, permanent and temporary emigration and fluctuating abundances suggested transient use and low site fidelity in an open coastal site. Transition probability estimates varied between sites. Estuarine dolphins visited sheltered coastal embayments more regularly than coastal dolphins visited the estuary, indicating a key metapopulation dynamic. We demonstrated that spatially structured subpopulations in a heterogeneous coastal-estuarine environment contained distinct suites of individuals and differed in size, demographics and connectivity and the utility of extending mark-recapture studies to investigate metapopulation dynamics. The MSCRD approach is applicable to species consisting of recognisable individuals and is particularly useful for characterising wildlife subpopulations varying in their vulnerability to human activities, climate change or invasive species.