Many coastal marine populations are made up of networks of discrete subpopulations of relatively sedentary adults linked by larval dispersal at the mesoscale (10–100 km). Patterns in abundance, and structure of populations at this scale are strongly influenced by the interaction of hydrodynamic forcing on larval dispersal with patterns in adult productivity and larval production. This issue is particularly important in the 14 fjords that indent the southwest coast of New Zealand, which present a highly fragmented and diverse array of marine habitats with strong gradients in benthic productivity, and with larval transport in each fjord dominated by estuarine circulation. Population structure of sea urchins (Evechinus chloroticus) was illustrated across this region by examining trends in size frequency distributions from 53 sites sampled in 2002. A consistent pattern was observed, with sea urchin populations from the kelp-dominated fjord entrances consistently displaying a large adult mode (mean test diameter 110–130 mm) with evidence for gradual recruitment of individuals into the population, while populations from the inner fjords showed two distinct patterns. At many inner-fjord sites a large frequency of recently emergent recruits 50–60 mm indicated strong recruitment events and high demographic variability, while at some sites populations had undergone complete mortality of the adult mode and at sampling were made up of only a single juvenile cohort. These patterns likely reflect a source–sink population structure across the benthic productivity gradients within each fjord. This has important implications for the efficacy of a network of eight new marine reserves (10,241 ha) and 14 commercial exclusion zones (46,002 ha) established within the inner fjords under the Fiordland Marine Management Act 2005, and for the sustainability of this fragmented marine system.