jats:titleAbstract</jats:title>jats:pKnysna estuarine bay in South Africa's Garden Route National Park is that country's most significant estuarine system for biodiversity and conservation value. One outstanding feature is support of 40% of South Africa's—and maybe 20% of the world's—remaining vulnerable and decreasing dwarf-eelgrass, jats:italicZostera capensis</jats:italic>, whose associated benthic macrofauna has been studied since 2009. For these invertebrates, Knysna comprises several significantly different compartments: sandy mouth; well-flushed marine embayment; poorly flushed central sea-water 'lagoon'; and two disjunct but faunistically similar peripheral regions–marine backwater channels, and low-salinity upper estuary. Although macrofauna ranges from dilute brackish to fully marine, its abundance, local patchiness, and over considerable stretches, species density remains remarkably constant; further, one-third of species occur throughout. Intertidally, all but peripheral compartments are low density and infaunally dominated, while some peripheral areas, and much of the subtidal, are higher density and epifaunally dominated. Overall, seagrass macrobenthos appears maintained below carrying capacity (e.g., by abundant juvenile fish) and of random species composition within a site. Two further characteristics are notable: Unusually, seagrass supports fewer animals than adjacent unvegetated areas, probably because of lack of bioturbatory disturbance in them, and the vegetation cover may ameliorate ambient habitat conditions. Unfortunately, continual heavy and effectively unpreventable exploitation for bait occurs, and chlorophyte blooms have developed because of high nutrient input. Knysna presents a microcosm of problems facing biodiverse and high-value habitats set within areas of high unemployment where subsistence fishing provides the main source of protein and seagrass provides the only source of bait.</jats:p>